The crates believed to contain L39 jet trainers ticketed for Nicaragua are missing from their resting place on the docks of the Bulgarian seaport of Burgas, Defense Department officials said yesterday.

The U.S. intelligence community, they added, has been put on the equivalent of an all-points alert to look for the crates. They could be en route to Nicaragua or be gathering dust in a warehouse in Bulgaria out of sight of U.S. picture-taking satellites.

If the L39s show up in Nicaragua -- and so far there is no hard evidence that they will -- the planes could easily be transformed into fighter-bombers to strafe and bomb antigovernment forces.

However, Fred C. Ikle, undersecretary of defense for policy, said yesterday that the bigger worry is that if Nicaragua received such weapons as L39s and MiG21 fighters -- which late last year were believed to be on a ship bound for that country but did not show up -- they would be used as a "bulwark" against retaliatory action by neighboring El Salvador and Honduras.

He said Nicaraguan military leaders have mapped a two-phase campaign. The first is to crush the rebels inside their country and then to increase support for Marxist, antigovernment forces in Honduras and El Salvador. During this second phase, Ikle said, aircraft such as the Czechoslovakian L39 and Soviet MiG21 would deter the Honduran and Salvadoran governments from "going after the source" of their troubles in Nicaragua for fear of being bombed.

"The planes would be a bulwark behind which to attack neighbors," Ikle said.

Critics of President Reagan's policy in Central America counter that the MiG21 is a defensive fighter that would not upset the balance in the region as administration officials assert.

Ikle said the U.S. effort to help El Salvador quell guerrillas in that country is going well but would unravel if Congress cuts off aid to the "contras," the antigovernment forces in Nicaragua.

Pentagon officials said they have no fallback plan to obtain money for the contras if further aid is banned. Ikle said private groups could not substitute for U.S. government aid in the long run, partly because after a while the question would become: "If the big U.S. government does not take an interest in this matter, why should we?"

If aid to the contras were cut off, Ikle said, "the real cost would come in two to three years when the expansionist phase begins" and Nicaragua "tries to destroy democratic government in the region."