A House-Senate conference committee on transportation appropriations yesterday smoothed the way for the Reagan administration to implement its plan to reduce the number of commercial flights at Washington's National Airport.

As expected, the conference deleted a House-passed provision in the transportation appropriations bill for fiscal 1982 that would have prohibited the Department of Transportation from reducing flights at National below the level of July 31. The congressmen who proposed the House wording had dropped their support for it after the airlines opposed to the plan reported that they had reached an accomodation with Transportation Secretary Drew Lewis.

As outlined by Lewis this summer, the plan would reduce airline flights from 40 to 37 each hour, allow nonstop flights of up to 1,000 miles from the current 650-mile limit, cap annual passenger traffic at 16 million and generally bar flights between 10 p.m. and 7 a.m. Because of the flight cutbacks mandated by the controllers' strike, the level of commercial flights is already below 37 an hour. Although the plan also would tighten noise limits, the effective dates are expected to be delayed by DOT.

The conference also decided a number of other transportation issues. Among them is Amtrak funding. Amtrak will get $735 million to run the national rail passenger network during fiscal 1982, but it also got something it didn't want. The conference accepted a Senate provision requiring Amtrak to reinstate the Cardinal, a train that used to run between Washington and Chicago through Cincinnati. Amtrak had discontinued it on Oct. 1 on grounds that it was a money-loser that didn't meet legislative standards for continued operations. Senate Minority Leader Robert C. Byrd (D-W.Va.) wanted the train back, and he got it.

Several issues important to the aviation community, and heavily lobbied, were also decided. For one, the conference decided to cut down on the amount of money some airlines are getting under subsidy programs designed to maintain service to small communities. One program, under which the government selects a carrier in a competitive process to serve certain routes and pays them for it, will remain intact.

The other program will be cut back significantly. Under it, some airlines in Alaska and some considered "local service" at the time the Airline Deregulation Act was passed, continue to get subsidies--an estimated total of $69 million this year--even though some of them may become quite profitable or grow substantially. Republic Airlines, for instance, got $42.5 million under this program last year even though its revenues totaled more than $1.2 billion.

Yesterday, the conference decided to terminate, 95 days after the bill is signed, all subsidies under this program that have gone for services to cities that board more than 80 passengers a day. In addition, after March 31, 1982, the conference will impose a cap of $14 million on such subsidies for the next six months for service within the lower 48 states and $5.4 million for Alaskan services. The cap doesn't apply for services that airlines are required by the Civil Aeronautics Board to perform.

Another provision limits the federal aircraft loan guarantee program to the purchase of aircraft with 60 or fewer seats. The program in the past had benefitted the newer low-fare airlines like People Express and Air Florida flying McDonnell Douglas DC9s and Boeing 737s.

The conference also decided that, for the time being, it would prohibit a controversial Civil Aeronautics Board order from taking effect in January. The order would prohibit U.S. airlines from participating in International Air Transport Association conferences at which the cartel members set fares on routes across the North Atlantic.