Most naval vessels move in groups/squadrons. Carriers basically always travel with a "carrier strike group"/CSG of a dozen other ships and destroyers often travel in "destroyer squadrons"/DESRONs. So any time you see a cluster of hits, just by the relative responses of each hit you can narrow down and guess the entire CSG/DESRON in one go and then work out which responses map to which ship in the CSG/DESRON once you have a good idea of which group you are looking at.

This is especially true because ships even within the same class have varying ages, different block numbers, and differing retrofits. So each one has a unique signature to it.

But also if you aren't completely certain you can always come back with a second high resolution pass and then it's trivial to identify each ship just visually.