Negatory skipper - the submarine should only be used as a battering ram in the strictest of emergencies, as a last-course of action - only to be used just prior to your passing...
But seriously, you are dealing with the OM with OMEGU versions of most of those vessels, just converted over by Fifi for Dark Waters, and as such, they can be difficult to sink. It takes some of them longer to sink than if they had one of the ship sinking models applied to them at double-strength... Once most of the gunwales go beneath the waves, you should "see" the ship-sunk icon on your NavMap. You do have to stay in the area to receive credit for the sinking though. I'll just about guarantee you though, that if you put another torp into her, it'll be 10x what you need...
