There's definatly been a good share of female captains, both human and alien, in TrekLit.
Vanguard had two, DS9 had captain Kira, and the female captain of the Gryphon (perhaps more that I'm forgetting). Voyager had Eden as Voyager's captain first, then as Fleet Captain. And there have been so much more in other parts.
There have been many female captains, but how many stories have they led? It seems to me to be relatively few. Voyager and Janeway is an obvious exception. There are many Voyager books.
I wouldn't mind an new ship with a female Captain even if it didn't have established characters.