Eh, you really overestimate the Druchii population numbers, and underestimate the size of the Black Arks. A few thousand cities of druchii is what you are saying they should have. That is a high number of cities from a mere province of Ulthuan's population in initial colonist number.
In general the druchii probably have more Black Arks than about two dozen. Using the magical number 8 multiplied by 8 for the number 64. I would assume the druchii created 64 Black Arks when they left Ulthuan. I want to say the druchii made 80 Black Arks, but that number has tens in it, and why a ten is not easy for me to explain. Eight times eight because eight is the magic significant number of the setting is much easier.
They probably could pop out a Black Ark a year, or every five years, heh, or every eight years. However, the population numbers, the rival schemes, the investment of resources. Everything required to keep the thing functional needs cooperation, druchii do not do cooperation. Either the creator of a new Black Ark is nearly as powerful as Malekith in influence, or is somebody's puppet.