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in SC1 in missions, enemies didnt just *poof* appear, the AI had to produce at their base.
I noticed in multiple missions now that enemies that routinely attack your base's dont get built but instead are spawned. This becomes evident when you take over an enemy base the dev's didnt anticipate you taking as the game is built for you to rush the missions. Then the enemies spawn inside the base and attack from within at set intervals.
In SC1 clearing out enemy bases would reduce/stop harassment but because of this AI at least in some missions it has no affect. The bases are effectively just for show and are a defensive barrier but not offensive.
Note I dont know if this applies to every mission, but I have noticed it on a fair few.