The one time Central Intelligence Agency spy ship Hughes Glomar Explorer reappeared in civilian dress yesterday as the deep-sea mining vessel that once was only its cover story.

The 618-foot ship, designed to pluck magnesium nodules off the ocean floor at depths over three miles, was unveiled here at the Bethlehem Steel shipyard, where it is being refitted for an experimental ocean mining voyage schedule to begin early in November.

Four years ago the Glomar was used by the CIA to recover portions of a sunken Soviet submarine that supposedly yielded valuable intelligence information. The ship has been leased from the U.S. Navy for 27 months by Ocean Minerals Co., a consortium formed last year by Lockheed Missiles and Space Co. with wholly owned subsidiaries of Standard Oil of Indiana, Royal Dutch Shell and a Dutch dredging company.

Lockheed officials are touchy about the former use of the ship, and made no mention of it during an elaborate press briefing and tour. But Conrad G. Welling, the ex-manager of ocean mining programs for Lockheed, who is now vice president of Ocean Minerals, laughed when he was asked whether Glomar might not bring back another submarine.

"This time we'll show you all the magnesium nodules," Welling said.

Regardless of what publicity the use of the Glomar might bring. Lockheed officials concluded that it was simply far better than any alternative ship.

The company keeps a worldwide inventory of ships suitable for ocean mining operations, and settled on the Glomar because it has, among other things, a lifting capacity of 14 million pounds, more than 8 times that of the next most advanced ship.

The ship also has a computer-run "compensation system," which provides a stable working platform even in high seas. A center well, running a third the length of the ship, provides a dry area for storing and preparing the undersea mining equipment. Two huge doors, which meet in the center of the well, slide back to allow access to the ocean.

For proprietary reasons, the ocean-floor mining machine developed by Lockheed was not in the well yesterday, when reporters toured the ship for the first time. However, the Glomar was being loaded with 30-foot sections of pipe, nearly 600 of them, that will connect the ship with the mining equipment working 18,000 feet below.

James Wenzel, president of Ocean Mineral, likened ocean mining to "standing on the top of the Empire State Building, trying to pick up small stones on the sidewalk using a long straw, at night."

The company claims to have spent $60 million on experimental ocean mining work since 1964, although Wenzel declined to give details. He did say that the financial problems encountered by Lockheed in the early 1970s led it to seek out partners for the consortium that is now Ocean Mineral.

By any standard, ocean mining is an expensive process and one that is still in its infancy. Welling estimated that Ocean Minerals will spend $150 million on research and development in the next three years before it would have "the confidence to proceed with the necessary capital investment."

The company's goal, he said, is to be in a position to have a fullscale Commercial ocean mining operation by the mid-1980s, when magnesium, nickel and cobalt are expected to be in an increasingly short supply on land.

The Glomar is expected to have little or no place in those operations. Advanced as its technology is, it will hold only 45,000 tons, including the mining equipment. Welling said the vessels used in commercial operations will be mammoth ships with capacities of 100,000 to 200,000 tons of nodules.

Like the Glomar, these ships will be used to dredge nodules from the ocean floor and pump them to the ship through huge pipes.

Magnesium nodules are black, potato-shaped objects about 2 inches in diameter that form around basalt, sharks teeth, bone or metal. Samplings from the ocean floor at various locations show they contain 25 percent magnesium and smaller amounts of copper, nickel and cobalt.

Except for copper, the United States produces insignificant quantities of these minerals.

Welling called nickel the key to commercial success of the operation, with the prospect of producing 50 percent of ocean-mining revenue. Though the present worldwide price of nickel is depressed, Ocean Minerals estimates that the mineral will be scarce and the cost of producing it on land very high by the time the ocean mining is developed in the next decade.

While nickel is a scarce mineral in the earth, it is believed plentiful in the ocean. Scientists estimate that, in the Pacific Ocean, where the Glomar will operate off Baja California, there are 1.5 trillion tons of the nodules.

Lockheed officials used the unveiling of the Glomar to take a new swipe at a pending text that is being used as a basis for negotiation at the Law of the Seas Conference in Geneva. Wenzel claimed it imposed restrictions on deep-sea mining that would make such operations commercially unfeasible. The restrictions are intended to guarantee that all nations share in the oceans' wealth.

The company is strongly backing interim "hard minerals legislation" that has passed the House and is pending in the Senate, where its prospects for passage in this session are considered fair. Among other things, the bill provides procedures for ocean mining pending ratification of the international treaty.

Welling said that if the bill does not pass it might cause Ocean Minerals to slow down the rate of its research and development.