I've had another interesting thought on the matter, 1.5 years later...
Vahki were constructed by Nuparu sometime before the war, and even before the Kanohi Dragon was set loose for the second time. Interestingly enough, we don't hear much about them during the Toa's battles with the Dark Hunters, but it would be reasonable to assume that their numbers increased exponentially during that time frame in order to assist with the defense of the city.
The war ends, and until the arrival of the Morbuzakh 2000 years later, there is never again another notable skirmish within or around Metru Nui. However, there are 5000 Vahki by the time of the 2004 storyline--five times the number of Matoran who would come to live on Mata Nui!
Makuta uses the Vahki to hunt the Toa Metru, press the populace into Matoran spheres, and oppress the Matoran in general. Perhaps a contributing factor in Makuta Teridax's lack of engagement in the Toa-Dark Hunter war could have been his desire to artifically allow the numbers of Vahki squads to explode and remain extremely high until his Metru Nui takeover, in which case he would have an unquestionably obedient and legal army at his back.