Usually a damaged ship that doesn't sink won't disappear. I've gone back for them more than once.
With lone merchants I hang around for a few hours, and if they don't sink after four or so I deliver the coup de grace. With convoys of course you can't do that. If I'm sure I sank a ship but don't get credit I just imagine that it limped into port a few days later and I'm just out of luck.
Love your sig, Sergei!