I work in the scientific satellite industry, and as far as I know, nothing is encrypted (possibly not true for military satellites). Sounds crazy, but I think people are more worried about reliability than security. Pretty much an accident waiting to happen.
Edit: It's more of a security through obscurity setup. The command codes aren't published (plus, they're protected under ITAR), and probably vary quite a bit per satellite. I think they are just hoping nobody takes the time to figure out what bits to send.