Best way to hit ships is not to assign level bombers against them. Level bombing maneuvering ships proved to overall be ineffective (as born out by quite a few attempts in both the Pacific and Med). Best way to kill ships is with dive bombers. Torpedoes attacks work to but tend to have a much higher casualty rate.
So as a CiC, if you have the plane types, best to assign a JABO attack versus ships. Level bombers will have a heck of time and it only gets worst the higher alt you make your run at.