With their submarines. One of the few parts of the Soviet navy in WW2 that was good was their submarine service. Imagine the problems the Japanese would have defending against submarines with torpedos that work and operating from bases closer than what the US had. Although the WW2 Soviet submarines were not as advanced as the Allies had they were more than enough to take on Japanese ships, both transports and combatants.How much of that did the Soviet's know? Also it's not just submarines that conduct merchant warfare, surface ships are actually a bigger threat. If the Japanese wanted to stop shipping with surface units how would the soviets counter them?