Like you said, SH3 is not reality. Two examples:
You can not reload torpedoes without a Weapons Officer, so you can't just leave that slot empty.
Surprisingly, you can maneuver just fine without a Navigator and/or a Bridge Watch Officer.
However, you can not change course without a Chief Engineer - you just get the "No Officer at Helms Station" error message.
These are just a few of the things about real u-boats that the SH3 programmers got wrong.
Lack of random crew rotations is another, although SH3 Commander reportedly incorporates that critical function.