Convoys and most of the ships that move in the game are scripted between waypoints. As soon as they reach them they vanish only to appear again at their original position (unless of course the waypoints are in a circle so they stay visible all the time).
In terms of the convoys it is practically impossible to script them getting into harbours are the strain on the CPU and the memory will be huge. Also it will cause problems in the game engine as I don't think it will be able to cope with so many ships in such restricted space.
BBW is the man to ask about this but I think this is the answer to your question in a nutshell.
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