Hitting the engine room to slow or stop a vessel is my standard technique and does the trick maybe 75% of the time, whereas hitting the bow has only "worked" for me on a few occasions - so I'm guessing there must be a degree of randomness built in. The last sinking of the game I've just left was an armed Large Cargo. I had one torpedo left (stern tube) so went for the engines, deciding to try to slow or stop it and then risk surfacing some way off to hopefully approach unseen and use the deck gun to finish it off. There was no need, the mid-hull hit sank the ship so quickly it had disappeared completely by the time I'd raised the 'scope again to check what speed it had slowed to. The GWX damage modelling suits me just fine!
I enjoy never knowing for sure just what hit will give what result.