Ships that have been damaged are 100% repaired again when they leave your 3D rendering range (as far as I get it). They also stop fighting when you don't watch them. So in other words, as soon as you leave the crippled ship, it's instantly repaired and on its way again.
I think this is a measure to save RAM (if all the thousand ships in the sea would actually interact with each others when they met by fighting or evading or what-have-you, I suppose we'd have one buggy game, though I'm not an expert on such things
), but it's pretty annoying some times.
So yeah, have fun sitting there for two days waiting for her to sink
!