Question: 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.
> 
> 
>

Answer: 
I might point out that in the movie, Picard is surprised that she was still alive. While she never appeared in the episode where he was assimilated, he mentions that her voice was always there and points out that ship and all the borg on it had been destroyed, to which she replies: "You think in such three-dimensional terms." 

One could theorize that perhaps the body that speaks is not the queen, but rather that the queen itself is a pervasive "personality" that exists throughout the entire collective and that she merely employs a body, whether it be a clone or a series of similar forms on each borg ship, to be her voice and to speak and act through when she has need to.

No canon to back that up, but that's always been my theory of her.
My wiew on Borg Queen is that she is not a real person but actually an avatar of Borg collective itself. An living embodiment of the whole Borg collective, put in one body. And that would explain how can there be so many Borg queens. The fact is there isn't really a Borg queen as a leader who governs all, but a living representation of the collective itself.