This bug is real pain... it ruins gameplay, realism and is difficult to fix. It was also present in SH4 and in some measure even in SH3 ( I remember tweaking a VIIC/42 and bringing it down to 400m. At such depth it slowly started sinking. I would like to see the .sim files of SH3 and search for clues, since the game engine is very similar at the core.
Dont worry, if I ever will be able to find a solution for this I will tell.
One last thing: do you know what the "put_on_water" thing is? How does it affect gameplay? It should have something to do with the physic model of the ship...
Cheers