I agree, had they returned they would have been just another enemy that becomes lamer and less threatening every time.
I agree that the overuse of a character leads to a loss of its punch. That is what happened to the Borg, obviously. However, I think one question arises here: in order for an antagonist to become a notable one, don't they have to appear several times? If they are seen in one episode only, as is the case of the "Conspiracy" creatures, they are indeed scary, but they can't hold that great of an importance. So, I think it's sort of self-defeating to say that an enemy becomes lamer the more it appears, because it requires several appearances to establish a character as a feared enemy. Well, that was a more general comment there.
I loved the grim idea behind "Conspiracy", but the stop-motion animation used to render the parasites seemed a bit inappropriate to me because it appears more suited for comical productions. It makes it too obvious that the creatures are a fabrication.