If you have a password-protected PDF and want to generate a decrypted version, it’s very simple with QPDF:

$ qpdf --password=123 --decrypt input.pdf output.pdf

To avoid entering the password on the command line (perhaps you don’t want it saved in your shell history):

$ qpdf @- --decrypt input.pdf output.pdf

Then enter --password=123 and hit enter and ^D.

To encrypt a PDF, do this:

$ qpdf --encrypt userPw ownerPw 256 -- input.pdf output.pdf

Similarly, to avoid including the passwords in the command, do this:

$ qpdf --encrypt @- @- 256 -- input.pdf output.pdf

And then type the user password, hit enter, the owner password, enter, and ^D.