There is "no likelihood whatever" that the Senate would approve SALT II as long as Soviet combat troops remain in Cuba, Sen. Frank Church (D-Idaho) said yesterday.

The chairman of the Senate Foreign Relations Committee made that prediction after hearing CIA Director Stansfield Turner and Secretary of State Cyrus R. Vance testify in closed session about the belated U.S. discovery of 3,000 Soviet combat troops in Cuba.

If Church is right about Senate sentiment, President Carter will have to consider the Soviet troops and SALT II in tandem to win approval of the treaty.

Church for months has been pleading with colleagues to consider SALT on its own merits, rather than link it to other facets of U.S.-Soviet relations. But he predicted yesterday, with Sen. Jacob K. Javits (R-N.Y.) asserting that it is too early to make such predictions about the Senate, that such decoupling is no longer possible.

Another part of the political fallout that started to settle yesterday over both Congress and the Carter administration as a result of the troops situation is fresh doubt about the ability of U.S. intelligence agencies to keep up with what is going on in the world.

Church, whose committee is in the midst of hearings on SALT II, said, "It has been my wish all along that the SALT treaty be unlinked [from other U.S.-Soviet relationships]. I've always stressed the SALT agreement should stand on its own merits."

A parade of senators made that link yesterday, with some of them demanding that Carter put SALT II and everything else on the line to get the Soviet troops out of Cuba.

The Soviets, said Minority Leader Howard H. Baker Jr. (R-Tenn.), "are thumbing their noses" at the United States.

"Unless we show substantial resolve and tell the Russians it's inimical to our interests" to allow 2,000 combat troops to remain in Cuba, "we will in effect be letting the Soviet Union thumb their noses at us," he said.

Sen. Richard Stone (D-Fla.) said SALT II and everything else the Soviets are interested in should be "put on the table" to get the Soviet troops out.

Saying there is a "total linkage" between those troops and SALT II, Stone asked, "If we can't keep their combat forces out of Cuba, where can we keep them out of?"

Javits, ranking Republican on the Foreign Relations Committee, said the Soviet troop presence may mean that "the SALT II debate will be somewhat extended. I hope it has no more serious effect."

Despite his hopes, Javits continued, the Soviet convert introduction of combat troops into Cuba "is hardly the kind of an earnest we expect as a prelude on the SALT II treaty."

Turner, in a brief appearance in the glitteringly bright reception room off the Senate chamber, refused to discuss what he told the committee, complaining that too many U.S. intelligence secrets had leaked out already.

But there was widespread agreement among senators who heard him testify in secret that the United States had suffered an intelligence gap by failing to detect, until last month, 3,000 Soviet troops who started to go into Cuba in 1976, if not earlier.

This raised the further question whether the United States could detect Soviet cheating on SALT II if the troops in Cuba had gone undiscovered for so long.

This latest intelligence gap, Baker said, results from "the reduced level of our intelligence," stemming in part from "a demoralized CIA."

Baker said that "we in the Senate must take account" of these shortcomings in considering SALT II. "If we can't find a Russian brigade with 3,000 troops" in Cuba, he continued, "I wonder" how the U.S. intelligence agencies could "verify Russian compliance" with the missile limits set forth in SALT II.

Sen. Alan Cranston (D-Calif.) immediately took issue with Baker on that point. Keeping track of Soviet strategic missiles covered by the SALT II, Cranston said, is a totally different situation than trying to figure out the nationality of troops spotted on the ground in Cuba.

Agreeing with Cranston, Sen. Charles H. Percy (R-Ill.) said the U.S. intelligence gap in Cuba "does not endanger or inhibit our ability to verify SALT II."

Sen. Jesse A. Helms (R-N.C.) said in a separate interview that the belated discovery of the Soviet troops dramatized "the lack of U.S. intelligence capability and to some degree a lack of candor" by the State Department.

Carter, as part of his effort to thaw relations with Cuban President Fidel Castro, suspended the flights of the SR71 Blackbird spy plane over the island in 1977. The Blackbird flies so high that Cuba's Soviet-supplied anti-aircraft rockets cannot shoot it down.

Besides lacking information from overflights, the CIA over the last few years has lost most of its reliable agents reporting out of Cuba. This has made the U.S. intelligence agencies heavily dependent on electronic intercepts, satellite photography and other mechanical spying.

One question facing Carter is whether to resume SR71 or U2 overflights in hopes of gathering additional information about the Soviet troops.