Israeli disappointment at limits the United States wants to impose on joint military initiatives by the two countries could result in an Israeli decision not to go ahead with the strategic cooperation plan discussed by President Reagan and Prime Minister Menachem Begin in September.

Both sides continue to express hope that the differences will be resolved. But Israel is understood to have made it clear that if the United States remains unwilling to go beyond the modest cooperative measures contemplated by U.S. policymakers, Israeli Defense Minister Ariel Sharon will not visit late this month to sign a proposed memorandum formalizing the strategic accord.

In addition, diplomatic sources said yesterday, Israel's decision to resume reconnaissance flights over Saudi Arabia, because of alleged U.S. refusal to provide it with intelligence data about Saudi military movements, is threatening to increase still further the stress troubling relations between the two countries.

Increasing nervousness within Israel about long-range U.S. policy intentions in the Middle East has been evident since the administration, in a bruising battle with Israel's congressional supporters, put across its plan to sell radar surveillance planes and other sophisticated aircraft equipment to Saudi Arabia. The tension was further increased when Reagan spoke in encouraging terms of a Saudi plan for Mideast peace that Israel regards as a blueprint for its destruction.

Now these frictions appear to be spilling over into the talks about the cooperation scheme that was intended to further administration plans for creating a pro-Western "strategic consensus" among friendly Mideast states and reassure Israel of American support.

However, since the idea surfaced during Begin's Washington visit in September, Secretary of State Alexander M. Haig Jr. and other administration officials have carefully emphasized that they are talking about limited measures such as the possible stockpiling in Israel of medical supplies for U.S. forces. In large measure, that cautious U.S. approach is dictated by a desire not to antagonize Arab states that Washington hopes to entice into the "strategic cooperation" framework.

On the Israeli side, Sharon and others have made clear their desire for more ambitious measures, such as the possible storing of U.S. weaponry within Israel and future joint maneuvers on a relatively large scale.

Sources on both sides agree, however, that Israel has been unable to get U.S. agreement for initiatives of that size and scope and has become increasingly disillusioned about whether the proposed agreement will have any real military value to the Jewish state.

An Israeli military delegation is expected here next week to continue talks on a memorandum of understanding spelling out the cooperative arrangements, and Sharon tentatively is scheduled to come to Washington about Nov. 29 to sign it. However, the Israelis have become increasingly bold recently about sending signals that unless the United States increases the size of its commitment, Sharon will remain at home.

There is some question about whether the Israeli threat is simply a bargaining tactic. U.S. officials were careful yesterday to insist they are assuming that a mutually agreeable deal will be worked out and that Sharon will show up on schedule. However, the officials also gave no sign that the administration is willing to move toward meeting Israeli expectations more fully.

Another potentially serious problem involves Israel's announced intention to continue flights it began last week over Tabuk, a Saudi military complex in the desert about 130 miles from the Israeli border.

Israel halted such flights in 1977 at the request of President Carter, but the Israelis now say Washington has not kept its promise to provide satellite intelligence about the Saudi military presence in the area.

Some U.S. sources believe the Israeli move has the broader aim of intimidating the Saudis and creating problems for the growing alliance between the United States and Saudi Arabia.

These sources said Washington has promised Israel whatever intelligence is necessary for its security but that Israel has rejected that offer as insufficient. The sources said there is growing concern that a continued Israeli hard line on the overflights, coupled with Saudi pressures on the United States to halt them, could become an increasingly serious problem.