After 96 hours without contact, the U.S. Coast Guard declared that El Faro, the cargo ship that disappeared during Hurricane Joaquin, probably sank during the storm. (Reuters)

Shortly before her hulking cargo ship, the El Faro, vanished in 40-foot waves with a single emergency ping, a young crew member named Danielle Randolph sent her mother one last e-mail: “There is a hurricane out here and we are heading straight into it.”

On Monday, after a four-day hunt for the lost ship amid the whipping winds of Hurricane Joaquin, the Coast Guard said the vessel had probably sunk in a 15,000-feet-deep expanse of the Atlantic Ocean. The few signs of its 33 crew members included a floating body in a survival suit and an empty lifeboat, barely visible in the waves.

The disappearance of the El Faro, in one of the country’s deadliest cargo-shipping disasters in decades, has devastated the families of its 28 U.S. and five Polish oceangoing workers, who regularly carted cars and groceries between Florida and Puerto Rico aboard a vessel whose name in Spanish means “the lighthouse.”

But it has also cast a harsh light on the dangers inherent in cargo shipping, the unglamorous but vital industry tasked with shepherding supplies across unpredictable seas. Maritime experts have begun to raise questions about whether the growing pressure to run fast, cheap routes could have persuaded ship leaders to ignore safer but slower courses that could have kept the vessel away from a battering storm.

“These guys went right into it,” said Bernie Marciniak, a retired cargo-ship captain. “Had he just gone straight down the coast of Florida against the Gulf Stream, he would have burned a lot more fuel. Had he gone the other way and survived it, his job might have been on the line.”

Cheryl and Eddie Glenn arrive said their son Sylvester Crawford was an engineer aboard the El Faro. (Bob Mack/ Florida Times-Union via AP)

TOTE Maritime Puerto Rico, the ship’s owner and a subsidiary of the Seattle shipping conglomerate Saltchuk Resources, said the vessel was routinely inspected for safety and pointed to a series of internal and third-party hull, machinery and safety checks earlier this year. Its crew, the company said, was made up of experienced mariners who had trained regularly on how to abandon ship and brave the rough weather common along its Caribbean route.

Commercial ships often launch from ports amid forecasts of storms because of the costs and risks of staying anchored, experts said. The company said it authorized the El Faro’s sailing “knowing that the crew are more than equipped to handle situations such as changing weather.”

But maritime experts such as Bill Doherty, a retired U.S. Navy captain who said he knew some of the El Faro crew members, said the 40-year-old freighter’s age could have compounded the dangers faced by tumultuous seas.

“That ship has been in extended life support for 20 years,” Doherty said. “It’s the ships that are beyond their safe useful life, it isn’t the people that are sailing them. They have got to be the best sailors in the world because of the equipment that they are faced with.”

The National Transportation Safety Board said it will investigate the loss of the El Faro. Responding to criticism from maritime experts, Mike Hanson, a spokesman handling crisis communications for TOTE, said, “All of those issues will be investigated in detail, and it will come out in due time.”

The El Faro ran a weekly supply route from the sprawling seaport in Jacksonville, Fla., to San Juan, Puerto Rico, a stretch of deep ocean long known as a “hurricane alley” for its warm tropical waters and history of storms.

When it sailed away from the Florida coast in the early-morning dark on Wednesday, the “ro-ro” ship — so named because its cargo of cars and industrial equipment could roll on or off — hefted 391 containers of food and basic supplies and 294 trailers of cars in its hold, a heavy load that experts said could have quickly thrown the freighter off balance in violent waves.

Vessels such as the El Faro “are very dangerous ships when you start getting some flooding onto the vehicle deck,” said Rick Spilman, a maritime expert and naval architect. But “the company wants to keep the ship sailing. You lose a lot of money with the ship tied up to the dock” or “if you go the long way around,” he added.

The El Faro, data from Vesseltracker shows, was one of six cargo ships to sail from Jacksonville on Wednesday, as forecasts for what was then a tropical storm warned of treacherous waves along its 1,200-mile route. But the company reported that the ship’s captain, an experienced deep-sea sailor named Michael Davidson, told the home office that his ship faced good weather and that “his crew was prepared.”

The 790-foot El Faro stretched twice as long as a football field, topped out at speeds of 22 knots (about 25 mph) and was built sturdily to brave hostile Alaskan seas. But by the time the freighter had neared the Bahamas, the storm had strengthened to a Category 4 hurricane with pounding 140-mph winds.

“Not sure if you’ve been following the weather at all,” Randolph, the 34-year-old merchant marine, wrote in the e-mail to her mother. “Winds are super bad and seas are not great. Love to everyone.”

At 7:20 a.m. Thursday, the ship’s crew told a Coast Guard command center in Portsmouth, Va., that the El Faro was taking on water, had lost engine power and was leaning 15 degrees amid four-story-tall waves — but that the crew was pumping water and that conditions appeared “manageable,” the company said. The ship would not be heard from again.

The Coast Guard and Navy launched surveillance aircraft, rescue helicopters and patrol cutters to search rocky seas across 70,000 square nautical miles, an expanse larger than the state of Florida. Two C-130 “Hurricane Hunter” planes built to fly at high altitude dipped below the clouds, hoping to call out to stranded crew members on short-distance radios.

On Saturday, one day after the ship had been slated to dock in San Juan, the crew of a C-130 spotted the first clue 120 miles northeast of Crooked Island in the Bahamas: an orange life ring with the El Faro’s stenciled marking. Within hours, as Joaquin blustered toward Bermuda, search crews facing calmer seas discovered an oil slick and a 225-square-mile field of packing foam, cargo and wooden debris.

Crew members’ relatives flew from across the United States and from Poland to a Seafarers International Union Hall in Jacksonville, awaiting word on the rescue and listening into daily phone conferences with TOTE officials, who said they had “the strongest sense of hope” that the crew was safe.

But on Monday, U.S. Coast Guard Capt. Mark Fedor said the vessel was believed to have sunk, though he added that search efforts would continue. “We are not going to discount somebody’s will to survive,” he said. Rescuers were unable to identify the lone body found by Monday, drifting in a cold-ready survival suit.

Cargo ships such as the El Faro burn an enormous amount of fuel, particularly when sailing into stiff winds, often helping to discourage companies and captains from pursuing a costly and unexpected change of course.

But one slight change could have made a big difference, said D. Peter Boucher, a retired shipmaster who also consults on maritime safety and accident reconstruction: steering the ship down the Florida Straits and turning into the Old Bahama Channel, passing south of the storm.

“It is tragic, because if he had taken that route and had the resultant power blackout,” tugboats “could have quite easily assisted him from South Florida ports,” Boucher said, noting that he sailed in this area for about 20 years.

Shipping companies, maritime experts say, often run older vessels because the federal Jones Act, which governs trade in U.S. waters, requires ships operating on coastal lines to be U.S.-built and -flagged. Updates to extend the life of a vessel — as the El Faro saw in 1992 and 2006 — are often seen as far cheaper than rebuilding a ship from scratch.

The five Polish mariners onboard also raised safety questions among shipping experts because they were what’s called in maritime lingo a “riding gang,” tasked with conducting routine repairs of the vessel while at sea.

Those workers are often brought onboard because they allow companies to save money by not taking the ship out of service. Some of those repairs can include working on essential backup systems in emergencies or systems that could potentially jeopardize the ship’s integrity or buoyancy, said Doherty, the retired Navy captain.

“Riding gangs . . . the minute I hear that, the hairs on the back of my neck stand up,” Doherty said. “It’s a cheap way of doing what should be done at shore. ... You have to be careful that the nature of the work doesn’t impact the sea-worthiness of the ship.

The El Faro was not the only ship roiled by Joaquin. Coast Guard helicopters on Thursday night plucked a dozen crew members from a life raft after their 212-foot, Bolivian-flagged cargo ship, the Minouche, began to sink near the Haitian coast.

The El Faro’s loss could prove to be one of the deadliest cargo shipwrecks in U.S. waters since 1980, when the Poet, a steel ship carrying 13,000 tons of corn, disappeared on a gale-tossed voyage between Philadelphia and Egypt with 34 onboard.

Those missing from the El Faro include a diverse range of civilian merchant marines and trained sailors, including Carey Hatch, 49, who last told his father to make sure the Florida State Seminoles football team kept winning.

The crew also counted at least four young graduates of the public Maine Maritime Academy, including Randolph, the crew member who sent her mother the e-mail warning of the hurricane.

Randolph was often one of the few women onboard her cargo ship, her mother said in a statement: An avid Barbie doll collector and “girlie girl” who loved to shop and bake. A few weeks before the El Faro headed to sea, she had changed her Facebook profile picture to a photo of her smiling in crisp dress whites.

Michael E. Miller, Julie Tate and Joe Heim contributed to this report.