Unlikely, most of the guests that were removed have other appearances on show that are still up, and most of them are his friends and long time supporters.
What is more likely is that they have controversial bit or two on them so they got flagged. There are episodes that have Joe Rogan say the N-word (not directed towards anyone and in-context, something he addressed today) could be that it was these episodes that were removed.
That is extremely unlikely to be true. The guests don't own the copyright, so they can't leverage that. Also, some of the guests are protesting this on Twitter.
This was my thought too but I can't seem to find anything from Spotify's new policy that touches on content removal for subjects unwilling to appear on a recorded podcast. Maybe legal disputes could be playing a hand here, however the timing is too convenient. Easiest answer seems to be Spotify is doing some cleaning on their yard after the recent backlash.