UNDER the gilded ceilings of St. Vladimir's Hall in the Kremlin, the leaders of the world's two great nuclear powers yesterday put their signatures to the first agreement reducing weapons capable of reaching each other's territory.The Strategic Arms Limitation Treaty (START), almost a decade in the making, will reduce the long-range nuclear arsenals of the two countries by about 30 percent. Though this falls short of the original goal of halving these nuclear arsenals, it is a leap beyond previous agreements, which simply sought to cap the number of weapons on both sides. In addition, the leaders of the two nations announced that they would convene a Middle East peace conference in October. (Related story, Page 3.) But the triumphant mood of the second day of summit talks was disrupted by the report of an attack on a Lithuanian customs post that killed seven border guards and seriously wounded one. The customs posts, symbols of the Baltic claim of independence from the Soviet Union, have been frequent targets of attacks in recent months in all three Baltic republics. The violence was the work either of unidentified squads of armed men, or of the infamous "black beret" elite troops of the Soviet Interior Ministry. Soviet authorities in Moscow have denied responsibility for the events and promised an investigation, but no action has been taken. The Baltic governments have demanded the removal of these units from their territories. Commanders of the elite troops also denied that their men were involved in the attack early Wednesday morning, an Interior Ministry spokesman told the Tass news agency. Soviet Interior Minister Boris Pugo told Tass he was "deeply shocked by the tragedy," and would "take all possible measures to find the attackers." At press time there was no reaction from either Soviet President Mikhail Gorbachev or President Bush to the events. Soviet observers speculate that the attacks were deliberately timed by conservative forces to embarrass Mr. Gorbachev during the summit by undermining his claim to be pursuing a peaceful solution to the Baltic demand for independence. Mr. Bush, in a speech delivered on Tuesday, strongly supported Baltic "freedom" and warned against the use of force, as occurred last January when 13 people were killed by Soviet Army troops in Lithuania. The two men and their foreign policy and security aides met for several hours at a state guest house in the countryside outside of Moscow yesterday before returning to sign the START Treaty in the afternoon. The agenda for these talks was focused on the future of arms control and security cooperation, as well as regional issues, primarily the Middle East peace process and the aftermath of the Gulf war. While both governments have declared their intention to pursue a follow-up START 2 agreement, neither side seems in a hurry to launch such talks. Instead there is a clear shift of the arms-control agenda away from such large and complicated bilateral agreements to more narrow subjects and to broader, multilateral talks such as those on controlling chemical weapons. Soviet officials have clearly indicated that the new phase of talks can even extend to military cooperation between the two countries. "In the center of the concept of the second stage of disarmament, we should have a total and new pattern of mutual security under conditions of openness and trust, under conditions of predictability," Soviet presidential spokesman Vitaly Ignatenko told reporters on Tuesday. This cooperation "will go beyond the framework of containment, and it will bring about a true partnership within the framework of a defensive pattern." One Soviet proposal calls for the joint development of anti-missile systems to be used against the launch of nuclear missiles by terrorists or third-world countries. Such a "defensive" project could give Moscow a way of handling the difficult issue of continued US funding and development of "star wars" anti-missile systems, which the Soviet Union opposes as a violation of the existing Anti-Ballistic Missile Treaty. Before the talks began yesterday morning, Soviet officials listed a number of areas which are on their arms-control agenda. These include the military use of space, tactical nuclear weapons in Europe, naval forces, and chemical weapons. Talks on cutting tactical nuclear weapons are expected to begin this year. These talks follow on the treaty eliminating medium and short-range nuclear weapons, the INF agreement, signed in 1987. This phase would cover so-called battlefield weapons such as nuclear shells fired from cannons. But even in this case many experts say the talks may not produce a treaty but a memorandum to withdraw such weapons from Europe. The proposal to hold talks on limiting naval forces is likely to be less well-received by Washington. The US has consistently refused to include naval forces in the talks on limiting conventional forces in Europe as well as Soviet bids to limit naval forces in the Pacific. The US has also rejected any inclusion of sea-launched cruise missiles in the nuclear arms agenda. Those missiles can be armed with either conventional or nuclear warheads and were used with the former during the Gulf war with great ef fectiveness.