Press the "Y" key, and look for your engines. If in red I think you better swim.
If not red them shut every thing down ( no battle stations, no silent running, no anything, even shut down radar ) Give everyone a 48 hour rest. Unless your in enemy territory then you still may have to swim ?
Best place to check though ( as said before ) is push the "Y" key and scroll all. I'm sure you'll find something besides the hull being all shot up. Otherwise WATCH out for those