Private universes, as we usually mean them (in particular, in the sense of a universe in which you don't have to abide by all the fiction rules), are not part of some "fiction multiverse" that includes the collaborative fiction universe, so no, they can't clog it up and yes, you can have any many as you like.
We're not going to arbitrarily force you to put all of your private fiction in one universe. The rules that we have tend to exist to make sure that collaboration is fair on everyone, so when you're not collaborating there's no need for them.