SH3 Commander is a program you should look into. It's a mod, but one of the safest ones since it has a very easy uninstall feature. Even more so, since it's a "front-end" program type of thing, the integration with SH3 is not as intimate and entangled (hence making it easier to undo).
Anyway, with it you can change the availabilty of different types of subs to more historical values. You can, for example, choose to start the war with a type IX-B allready
... It has a lot of other cool features too, and the best of all is that they're all optional; just choose the ones you like, leave the ones you don't. For that reason, it's the best mod around (allthough clearly not as extensive as other mods out there)