Ok, looks like i got the point. Any travelling ship (except the named ships) must have a few instances becouse if you sunk it, it have to be respawned, say, for next patrol, but as docked ships not move, they cannot be deleted, then they have just 1 instance for layer. Big thanks to Propbeanie and KaleunMarco for help
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I thought, may be it's simplier just to make the ship like corvette patroling inside the harbour to protect it, how it affect a performance and possible CTD? I just didn't see it in any SH modification.