Try hitting a ship in the stern to destroy the propellers. It won't slow down and stop as you want right away. It might take longer than you think it should but it will stop. Out on my last patrol it hit a freighter in the stern. Just to see what damage I did I used the external camera and found out the propellers were not turning at all and there was a huge hole in the stern too.. Ship kept on moving just the same from inertia. Same thing happened hitting an escort in the stern. If you can wait long enough the ship will sink stern first, but it takes a long long time. OHII and the critical hits mods are what I believe makes this happen now. Could be another mod helping but I'm not sure which one it is. Just be patient if you're using these two mods and you'll see what I mean.
On the other hand I've hit escorts coming in head-on to my Uboat [with magnetic pistol] and put a hugh hole in the bow. She kept moving but by doing so would take on water and sink bow first. Again it will take a long time, but sink it will. Actually I been using the magnetic setting 90% of the time with more successful hits.
Here's the freighter hit by only one torpedo in the stern heading for Davy Jones' Locker.... stern first.