Were they meant to be the same entity?
If they weren't, does this imply that Borg have distinct "hives"?
Out-of-Universe, the actresses playing the roles were all mixed up, but sounds like Paramount originally wanted the same actress implying it was the same Queen (or merely that all Queens are 'clones'?):
From http://www.imdb.com/name/nm0860749/ (Susanna Thompson):
Trivia: Got the role of the "Borg Queen" on Star Trek: Voyager only because Alice Krige (who played the role in the movie Star Trek: First Contact) refused to reprise her role.
For the final episode, Susanna Thompson was not available (because of shooting Once and Again) so Alice Krige played the Borg Queen in the final episode.