A lot of them do disappear when they reach that last waypoint. It is adjusted in the Mission Editor, and can be changed.
If the ship is written directly into the SCR (Scripted) layer, it will stop and sit there if it is set to not delete. If it's in the RND (Random) layer, then you might have it generating several times during a game, and all of them ending up colliding as they reach the end. At least I think that's how it works.
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