As a long time GWX fan, I recently made the transition to SH4 when the sub-bug bit again, and yeah, I was a bit curious about the ship sinking in TMO as wel.
From my (limited) understanding, TMO doesn't change ship sinking mechanics much from stock, it concentrates on other areas. This was a bit disappointing, but after comparing TMO and RFB, I decided I still preferred what TMO had to offer in other categories so I gave it a go (alongside RSRDC).
After one war patrol sinking a few ships I was, indeed, somewhat disapointed with how quickly the ships sunk. So I dug around and found this thread.
http://www.subsim.com/radioroom/showthread.php?t=193610 Which has a supplemental longer sinking mod for TMO, seemingly largely achieved by reducing how much HP damage the torpedoes cause.
Well, after installing it I'm in the middle of a new war patrol (same career) and I've sunk three 5000 ton ships, including a Kuma CL, and they've all sunk in about the same time. Maybe I'm using overkill though, as I've hit each ship with two torpedoes (more than I know it probably needs, but I'm leery of early-war Mk14s causing me grief, and indeed, that Kuma would've eaten 3 torps, but one detonated early). To be honest, I haven't noticed too much of a change, though I guess the first freighter took a bit extra time to sink, and (I think) was listing before going down, not much though (a minute at most). The Kuma and the second Maru sink almost immediately, but in the second Maru's case, that might be because it suffered multiple violent explosions, must've been carrying something volatile.
Honestly, despite the small sample size, I'm kinda wondering if I'm just using overkill (2 torps on a 5000ton target) or if its just the way TMO is, even after that mod. If its the latter, then I guess I'll just keep at it, since TMO is quite nice otherwise. I'll also admit I never played stock SH4, so maybe ships sink even faster in stock. I really do miss the ship sinking style of GWX3 though.
Either way, Silverdragon, you could try out that mod I linked and see if it improves things for you. It is too bad the guy who made it never uploaded that new/tweaked version he mentioned he would. Life probably just got in the way.
[edit] You know, I think the thing that bugs me the most with the way they sink is not the speed at which they sink, but that they always seem to do so nose or stern first, they never just list, roll over, and go down on their side before starting to tip one way or another.