The reason they are rated low, for me, is as follows:
1) Submarines are expensive
2) Submarines die to fighters without risk to the fighters
3) Submarines purchased take 4 full turns to break even (odds?)
4) The two submarines in SZ 5 die in every game I’ve ever seen. It’s just a debate over when, not if they die.
5) Germany has no business buying up lots of submarines.
6) America is relatively unaffected by U-Boats. Sure, they have less money, but honestly, -3 IPC from 42 IPC is not that much.
Those are ranked in order of importance to me.
That said, if you get them as a random bonus, it isn’t horrible. Germany, of course, has no worthless advantages.