You've hit upon a very important point! Indeed, availability of merchant shipping was a critical issue for Japan at the outbreak of war in Europe. Even during the War in China, military demands on Japanese merchant shipping had been extremely detrimental, with shortages becoming commonplace, and impeding the normal functioning of the Japanese domestic economy. By mid-November 1940, the Japanese domestic economy was already operating with only 75% of the shipping deemed to be the absolute minimum necessary to maintain the economy. Shipping shortages would go on to plague Japan throughout the war, even before the American submarine blockade began devastating what merchant shipping the Japanese did have, and would prevent Japan from ever fully digesting or integrating the resources it went to war to acquire.

But let's zoom out a bit. At the time of the outbreak of war between Japan, the US, and the UK in 1941, the Japanese merchant marine consisted of about 6.7 million tons of shipping, and Japanese estimates budgeted a minimum of 3 million tons of shipping in order to sustain the civilian economy. Yet, even so, about 30% of Japanese trade was carried on foreign flagged vessels, which only increased the stress carried on the increasingly limited Japanese merchant shipping, even assuming no war time losses. Issues of shipping were indeed a major concern for Japanese policy makers and warplanners, as the need for merchant shipping to be shuttled around between military and civilian used imposed stricter timetables on Japanese operations than they may have liked, as the same transports being used to carry troops south would have to be returned to the domestic economy. Allocation of shipping resources between Army, Navy, and civilian use would be a major sticking point throughout the war. As an example, at the outbreak of the war, the Army and Navy combined had commandeered 4 million tons of shipping to support initial operations (you will note that this leaves a mere 2.7 million tons for civilian use, less than the 3 million estimate required to sustain the economy). The Army pledged to return 1.1 million tons of shipping to civilian use by the end of initial operations over the course of 1942. As the war continued, developing into the Solomon Islands Campaign, the Army demanded additional shipping be allocated to it in order to support operations against Guadalcanal, a request that was rebuffed by the War Ministry and government. The dispute over shipping allocations escalated into a fistfight between the head of the Army General Staff's Operations Department and the head of the War Ministry's Military Affairs Bureau, while also including a shouting match between the former and Prime Minister Tojo the following day.

As you can see, to say the issue was contentious is putting it mildly.

I am not aware of any American or British shipping commandeered by the Japanese early in the war. For the Americans at least, as part of efforts to reduce oil exports to Japan short of a full embargo, the US government had asked private corporations to redirect American flagged oil tankers from trade with Japan as early as the summer of 1940. Yet, you are correct in pointing out that there would be severe issues in crewing new merchantmen. Quality of merchant crews was a major issue for the Japanese, especially as many of the experienced mariners and seamen who made up the backbone of the merchant marine were also part of the naval reserves, leaving only inexperienced crewmen left to man Japan's merchant shipping.

The question then becomes: why? Why was Japan in general and the IJN in particular so unprepared for the mercantile demands of war? In many ways, they had done their best to prepare, but the best Japan could do was simply not enough. Throughout the 1930s, the Japanese government had invested heavily in expanding and modernising Japan's merchant marine via governmental subsidies. The Japanese merchant marine expanded by around 2 million tons from the early 1930s till the outbreak of war, and--due to a premium placed on modern ships--many of these merchant ships were large, efficient, and fast (especially as some were designed for easy conversion into aircraft carriers). At the outbreak of the Pacific War, the Japanese merchant marine was third in the world in terms of size but possibly first in terms of quality. Similarly, the issues of oil were well known. Between 1934 and 1940, Japanese ocean going tanker tonnage went from 120,000 tons to 364,000 tons, and capacity grew from 1 million tons of oil to 4 million, carried by a fleet of tankers that included some of the largest in the world at the time. Impressive as these increases may seem, it simply was not enough for what was being demanded of it.

Part of the issue was simple institutional blindfolds in the IJN. As an institution, the IJN prioritsed offensive action and battle above all else. The best officers and men strove to receive combatant commands, and tended to remain there, leaving only officers and men deemed less capable to take up rear area commands. There was no rotation between officers in command of combat units and those tasked with supplying them. In the IJNs naval planning, there was little concern on whether the logistical ability to carry out an operation existed. Rather, it tended to be that the operation was decided upon first, and then logistics commanders would have to find some way of supplying them. Logistics was never the IJNs (or the IJAs) strong suit. In addition to the institutional issues described above, the IJNs grand plan for war with the United States only involved a single campaign culminating in a decisive battle. Thus, logistical concerns would take some time to come into play, as--presumably--by the time questions of shipping commitments or supply lines came to a head, the American fleet would be at the bottom, and a victorious Combined Fleet could return to its home bases.

I'm afraid I don't have much to add on the Soviet trade aspect of the question. Regardless, I hope this response has helped answer your question, and please feel free to ask any follow ups.

Sources

• Michael A. Barnhart, Japan Prepares for Total War: The Search for Economic Security, 1919–1941

• Edward J Drea, Japan's Imperial Army: Its Rise and Fall, 1853-1945

• David C Evans & Mark R Peattie, Kaigun: Strategy, Tactics, and Technology in the Imperial Japanese navy, 1887-1941

• David C Fuquea, "Advantage Japan: The Imperial Japanese Navy's Superior High Seas Refueling Capability", in The Journal of Military History.

• Alan D Zimm, The Attack on Pearl Harbor: Strategy, Combat, Myths, Deceptions