If you have enough money you can build a system that is technically encrypted. See Fusion, d-star, and the other one I can't remember.
What the FCC doesn't want is message passing that is not decryptable by them. They could care less if me or you can't decrypt fusion with an sdr.
An interesting grey area is pactor. And not just for encryption, but also "symbol rate". If anything is going to bring ham radio into this century kicking and screaming it is stuff like aprs and pactor; and I say that knowing how awesome JT and wspr are.