SH3 is aimed at the battle for the Atlantic where the main task of german subs was to disrupt merchant traffic and nothing else. With the mods available from the community (and the much awaited GWX coming soon) I think imho that SH3 will be right on the spot and a fantastic experience.
During WW2 the purpose of subs was not to hunt other subs. If I want to do sub hunting, I shoot up DW...
I don't have at hand the stat on how many subs were actually sunk by another sub during WWII, but I would guess it must be a very low figure as I never read about any. (But I am not a Pacific specialist and not much interested by this theater besides carrier operations)