I'm pretty sure it was a raw issue and could therefore be brought back if you're thinking of modding them anyway. If I recall correctly, the problem was caused by MOSQUITO having [CLUSTER_NUMBER:100:200] and GIANT_MOSQUITO having [COPY_TAGS_FROM:MOSQUITO]. And, if I recall correct, it was resolved by adding [CLUSTER_NUMBER:1:1] to GIANT_MOSQUITO. So, remove [CLUSTER_NUMBER:1:1] from GIANT_MOSQUITO and you should get the flocks of 100-200 giant mosquitoes again. (This is in creature_bug_slug_new.txt) That said, most players concluded that the mild nuisance they were as a sort of substitute for badgers (in frightening dwarves) was nothing compared to the nuisance they were as a sort of substitute for catsplosion (in devouring FPS), so you might instead want to change [CLUSTER_NUMBER:1:1] to something like [CLUSTER_NUMBER:50:100] (rather than removing it so as to use MOSQUITO's 100:200) among other changes if you want to make them some sort of threat to be fought.
I recall that around the same time there was a bug that vampires, which are supposed to accuse others of their own crimes in order to throw off the trail of justice, would accuse wild animals. These two bugs combined were the butt of some jokes that, along the lines of the yak general, sometimes the "bug" would have made sense -- i.e. if Urist is found drained of blood, how implausible is it really to blame the giant mosquitoes that swarm over the fortress like a biblical plague?