Probably not, the hypothetical is that the IJN uses its submarines more effectively, not that the USN takes up the historic tactics used by the IJN.
Just how big was the IJN submarine fleet? And how many of the subs they had were true oceangoing warships? Given that the Pacific is a much larger expanse than the Atlantic, and the IJN didn't have the luxury of taking over a series of industrialised neighbours to provide forward bases, I think they'd have had a very hard time stopping the enormous flow of supplies form the US to it's fighting men.
The slow down for the ETO was already in full swing by the Okinawa campaign. I read the book operation downfall and it went into detail on this. The US was gearing up for the invasion of the homelands of Japan and what was in the ETO was all they were going to get. As Darren said also the Pacific is a big ocean. The supply lines would have gotten longer but Japan would have to had a much larger sub fleet to have the commerce war that the US operated at the bigging of the war.
I agree with crzyhawk, the B-29 had a huge range but without the fwd bases the US used, they were unable to bomb Japan, atomic bomb or not. A huge submarine force is not necessary to wreak havok with shipping, merchant or warship. Although the is obviously way more risk when warships are involved, as a Submariner I can tell you that it isn't as easy to find a sub as it appears. A couple of subs operating together, attacking merchantmen or troopships orany ships causes huge confusion. And since I-400 is fast submerged she shoots, dives deep and away, the second boat does the same and the escorts become unsure where to go. The odds favour the sub, especially in water that is deep. Once they get below the layer, it's all over. If the escorts don't have a decent location fix on the sub by that point it is doubtful they will. I can tell you how many times I have been in an exercise and we evaded the surface units and came back and fired again. And the O-boats we used were not teardrop hulled nukey boats, thet were 25+ year old diesel boats. J
