Subs or no subs?
It's a fairly pointless question, because if Imperial Japan had never embarked on building submarrines/never been sold submarrines post Great War, then she may have never gone to war in the Pacific because she wouldn't have been a 'Great Naval power'...
...Or rather the Imperial Navy would have had far less say in many matters in the lead up to milliterisation from 1935-1940, hence the 'Advance South Policy' may never have got off the ground.
It's a fairly big butterfly to get rid of the submersible branch of the Imperial Japanese Navy, even if it didn't have the prestige of the other vessels of the fleet.
I actually think that Imperial Japans doctrine for submarrine usage was about as good as she was going to get. On the procurement side of things, there was a lot of effort wasted in producing smaller submarrines and of far too many types. The admiralty should have concentrated on the large and medium ocean going designs, and used them more or less as they were used, but perhaps been a lot more flexible in creating a seperate form of co-ordination for submersible use, rather than viewing them as an extention of the surface fleet and relaxing engagement rules.
In terms of developing a commerce raiding submersible fleet, I doubt it would have Imperial Japan any favours, nor would have it advanced their war effort significantly.
While the midgit subs Imperial Japan produced were technically capable, they also didn't do much damage anywhere. I can only think of the Sydney harbour incident off the top of my head where they were successful.
Part of the trouble is that the Japanese developed them partly as a 'submersible torpedo boat', and hence thought that it may be good to use them in close in coastal defence. Hence many were lost unaccounted for. In reality the best use of such vessels in the era was harbour infiltration, yet following becoming the 'masters of the pacific' there were very few harbours they were left in range of that they could infiltrate.
Hence the ~300 midgit submarrines Imperial Japan ended up building over the war years ended up being a waste of resources overall.