I don't think it's true of all villains/characters, just some of the ones with savvier negotiatiors. (Although I do know that it was standard practice for the Virgin books to have all characters, including new companions, to be property of the authors, with Virgin having permission in perpetuity to use them.) The Daleks have always been a special case. I would be surprised, for example, if they would actually have made a 4 second, non-plot critical cameo by the Macra in Gridlock had they needed to make a whole separate negotiation for them. I do know that Moffat has said that one of the things he wants to do is focus more on new threats and less on returning (although he didn't name names.) I doubt that means NO returning characters, but hopefully we've seen at least the end of the period where the Daleks show up every single season, and starred in 3 out of 4 season finales. I liked the balance from Tom Baker on, when each Doctor would have one or two run-ins with the Daleks and Cybermen. If only JNT had been so sparing with the Master.
Actually, that's absolutely right on almost all counts. I did a little checking (my sister is friends with one of the writers on current WHO) and seemingly, how it worked was that distinctive menaces with distinctive designs (that is, someone had to come up with a lot of production work) are partly owned by their creators. So, off the top of my head, I'd guess the obvious ones (Daleks, Cybermen) and maybe some others (Ice Warriors, Yeti, Draconians maybe, Chumblies...that was a joke, son!). When the new series was a go, the BBC entered into negotiations with Terry Nation's estate and, instead of the usual "period contract", got a flat use fee (this was negotiated so close to production that the episode "Dalek" was jokingly referred to as "Absence Of The Daleks" in case the fee wasn't worked out in time) - which, I bet, paid Terry Nation's heirs very hansomely (and they only stand to benefit if the return was a hit, what with marketing fees for spin off toys, etc.).
But Moffat, as stated, wants to see about returning some new villains (I'm betting Ice Warriors and Daemons) and he finds the Daleks, to paraphrase, "a bit naff" - so yes, Dalek-less (or at least Dalek-Lite, now with less strontium) times are probably coming soon.
I'm hoping the new actor and show runner might mean a bit of a turn away from some of the "fan-service" that's gotten a bit out of control in the last season.