There is a thread somewhere here that talks about an up coming mod as part of GWX that lets you mess with trim. I don't know if there is a way to seal off a compartment that's totally flooded. I agree with Bookworm_020 that control and disruption would almost certainly scupper your chances of actually getting home, let alone fighting a battle.
I found this site which talks about salvage operations for flooded/sunk submarines which was completed by the USN around the end of WWII.
http://www.maritime.org/fleetsub/air/chap6.htm
In reading this I guess it might be possible to get underway with a submarine fitted with this sort of system, but I don;t think you'd want to be messing with this whilst under attack. I don't recall reading anywhere about uboats having such a system.:hmm:
Anyone else know if they carried this sort of equipment?