Well, that entirely depends on who are they fighting against. IIRC (and you mention it also) IJA had their own fleets of supply ships, so in that aspect they were totally independent. Given that Korea is at spitting distance from Japan, I imagine most of the time they could be protected by land based airplanes, controlled by the Army. I don't really see anyone with enough sea power to challenge their supply train, which I presume would be the only important thing in such a war. The only power that could actually challenge Japanese on Asian mainland in Korea and Manchuria was USSR.
USSR probably had a number of subs in Pacific fleet, so, I take it for granted that they would attempt to interdict the shipping supplying Kwantung army. How successful would they be? I'll go out on a limb and without really thinking about it, I'll declare that it would not be decisive. Specifically, I do not see the war lasting long enough for the effect of interdiction to come into play, if the USSR starts it and is fully prepared.
IJA, if it starts will most probably be slaughtered as at Nomonhan.
IJN would make it a matter of principle to clear the seas around Japan, regardless of their relation with the Army, while they will both (Navy and Army alike) probably bomb Vladivostok, where subs are based and attempt to make it impossible for them to sail.
But most likely, the effect will not be important, since Red Army will sweep the Japanese off the continent.
I do not see who else could make war against IJA in Manchuria, except Chinese, eventually if the US is not at war. By the time this would come to pass and if the Chinese are able to endanger Japanese positions in Manchuria and Korea, I presume Japanese Army will be in no shape to offer any meaningful defense. EDIT: Oh, forget the last paragraph. I didn't see the 1940/41 part.