Crannogman has it right. The ships aren't just a random distribution. They spawn at and despawn at ports. Not actually at the docks, but fairly close.
The big exception is the set piece battles, like midway. They spawn a *long* way from the battle, but not actually in ports. The do go to ports when their part is done though. I'm just guessing here, but I suspect that getting the timing of the ship movements for the battles down perfectly was just too much work when spawning them all the way back at port.
If you want to see for yourself, open up the .mis files with the editor. They are in "\sh4\Data\Campaigns\Campaign". The yellow diamonds are spawn points.
As an aside, I have never gone out of my way to watch any of those set piece battles. I really should one of these days. The only time I've actually seen one by pure chance was in SH3+GWX. I was harbor raiding during the invasion of norway and all of a sudden, some german surface vessels showed up and starting shooting everything. At first I thought they where enemy destroyers bearing down on me and shooting at my periscope the way destroyers do in these games...
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