She was on the throne when I checked with a Naked Recruit start. I have updated this page with the location of Naked Command, the Capital of the Naked Union. It's possible that bandits caused her to aggro to a different part of Naked Command, and she probably goes somewhere else to sleep at night maybe. Let me know if you are still unable to find her.

thinking of using this as a new game+ mod, I can't find the queen though I checked every floor of the faction command