I have to say I agree with you Alexdk. I posted something very similar in my Ship won't Sink thread. First patrol I did manage to sink two boats with one torpedo. One did take a little bit to sink (like an hour). The other actually went down immediately. However, another boat took two. On my second patrol I found a small merchant, hit it perfectly with a torpedo right mid deck below the smoke stacks, 12 hours later, it's half sunk but not sinking any farther. The water is literally passing over the hull and at times an entire half is submerged due to waves, but when the waves aren't there you can see its not sunk any further than it was 10 hours ago. Absolutely crazy.
I have to say I really love how SH3 Commander offers a few tweaks. GWX is absolutely incredible but I too would love it if it were a bit customizable. I don't even have realistic ship sinking times turned on and still...12 hours and this 3/4 sunk ship won't go down.
Basically I would love to know if there is somethin I could tweak as well. Personally I'd love to see a little more one hit firey explosions
Oh, and I am running all latest patches. GWX, SH3, SH3 Commander, etc.