Most NDAs aren't very lenient to stripping protections one of the parties has put on its data. Protected PDFs aren't really consumer products like video and audio, you usually want to follow the rules.

Protected PDFs are how most technical e-books are distributed.

How do you do that for simple password protected PDF's ?

Elcomsoft makes a product that can do it. They charge money, of course. Free alternatives can be found, if you care to look for them.