the problem is they didn't bother to create damage files for things like sailors and most of the guns in the game so the only way to destroy them is to destroy the deck they sit on. but this gets more difficult because many ships have incomplete or non existant damage files for many parts of the ship so while you might get lucky at times, for the most part, the only way to stop the guns is to kill the whole ship so it registers as destroyed.
same thing goes for shore guns, I have had fun shooting them and 2 out of 3 you can destroy but often there is one or more that you cant kill even with a direct hit because the game has no file to register it as destroyed
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