Just to comment on the flooding after repair issue .... it's on my list of things to try and work out the root cause and then fix. It may be a hardcoded damage zone issue .... not sure at present.
As Darkfish says, the realistic damage scenario is one of the biggest priorities for the TSWSM. Here's a list of functionality we've built up in terms of damage, it may not seem that spectacular - but it takes a lot of work to get all this working for playable surface ships;
1) Weapons which stop working when damaged / destroyed (big issue for German units).
2) Creating a Magazine which will really take your ship down if destroyed.
3) Radar which stops working when damaged / destroyed.
4) Engines which slow and stop in proportion to damage.
5) Damageable torpedo launches (where the ships had them).
6) Damage which makes the ship list, but not sink (you get a kind of limp home mode).
7) Damageable (with leaks) fuel tanks.
8) A compartment & armour layout which looks like a surface ship and not a submarine.
9) AI Warships which sink when absolutely batterred by surface fire (some stock damage models will only take a ship down when hit by a torp below the water line) ... this is a biggy and is taking hours.
10) Preventing AI warships from saying they're destroyed before they actually sink.
11) Preventing many AI ship from taking damage in the rough seas environment we've created/ R using - all ships actually look like they are having a rough ride in extreme weather.
12) Almost forgot ... all damage shows up in the damage control screen.... so you can see whats really going to kill you