Like much else in the game, this feature is probably broken. Don't get me wrong, I love pacwar and I think it's a classic, but it's also a bit of a mess internally and hasn't been actively worked on for more than 20 years.
I have to say though, I wish WitP was closer to this level of playability. I own WitpAE, but find it irritating beyond belief due to the UI. It simply should not be so difficult to e.g. order some ships to go somewhere and load a unit onto them, at the grand strategic scale. Armed forces have staffs for this sort of thing--much less unreasonable in pacwar.
As Allies I wouldn't worry too much about the alleged range of your SS, base them pretty much anywhere safe and stick em around the main convoy areas, and you'll clean up mucho shipping. Coastal SS are fairly useless for both sides AFAICT (soon spotted and attacked and/or neutralised usually), but the ocean going SS for both are reasonably effective--Allies extremely so from mid 1943 or so, JA decreasingly so from that time, which is reasonable.
SS range perhaps seems to matter more for the Japs, but I have no scientific reason to think this, it's only an impression from playing the game a fair bit back in the day. It may have more to do with the supply state of their base, but who knows eh?? However if that's the case then perhaps make sure there are LCU and air in a sub base to make sure there are plenty of supplies and fuel. The supply convoy algorithm seems to 'forget' about otherwise empty bases from time to time and they run down to nothing. Again, just an impression...