Umm, what what? The Borg assimilate people and starships. After a victorious battle, no doubt the assimilated starships were put to good use as kernels for future Cubes, and the assimilated people were utilized as their crews.
I find it hard to believe the queen was tricked into regenerating along with all the drones.
Then again, when Her Drones went asleep under foreign command, that would be a perfect time to scuttle and run.
As for "astral plane", there's every indication that the Queen is a software entity first and foremost. She just has access to bodies - a cloned supply of those, as we see alternating Krige-Thompson-Krige-Thompson bodies...