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If I recall correctly the Japanese did not subscribe to the idea of using subs to hunt logistical ships and instead focused on having submarines target warships. They were particularly banking on their advantage against the Americans in torpedo technology. Their torpedoes ran on oxygen, which produced little to no bubble trail (which made them very hard to detect and dodge), whereas American torpedoes ran on carbon dioxide(which did produce a trail). Basically hoping they could score some big torpedo wins against American warships. As the war progressed and they lost ships, submarines actually filled in as logistical ships that tried to sneak by American wolfpacks and they started thinking about the idea of using a submarine aircraft carrier (I-401) to launch surprise air-raids in American bases on the Eastern Pacific.
Here is a pretty nice article describing how despite having a world-class submarine force Japan failed to perform well with it. https://madmonarchist.blogspot.com/2016/12/japanese-submarine-campaign-of-world.html
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Great article, also:
There were lots of ships going from the US to Russia so sinking them would be easy.
However Weinberg in World at Arms argues very convincingly that the Soviet Union and Japan had a tacit agreement that if Japan would let the lend-lease convoys alone the Soviet Union would not allow American bases on in Vladivostok and other really close to Japan bases.
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