We've discussed this issue a few times before without coming to a completely solid conclusion.
I think it's hard to draw a definitive line on this issue. On the one hand, as nonniemouse stated, the term "zako" means "small fish", and in this context it refers to the expendable, low-level female minions rather than a high ranking individual villainess, much less an evil queen. However, could a named, individual villainess also be a zako? I think so, as long as she is still a minor character who is treated more like expendable cannon fodder rather than someone important or high-ranking.
There may be a "zako" spectrum, with cloned or nameless minions on one far end being clearly zako, and named, individual but still minor minions being more towards the middle (but still zako), followed by the higher-ranking villainesses who are more on the other side but who may still have a few "zako" qualities (being treated as expendable by their boss, for example), and the evil queen or arch-villainess type being on the far opposite end of the spectrum. So I definitely don't think it's required that a female enemy be cloned or nameless to be a zako, but those are both qualities that are strongly associated with zako.
Regarding the evil queen and arch-villainess types, I agree they can be interesting, but they probably belong in a separate thread rather than in the main "zako" thread.
Other thoughts?