How do I find password-protected PDFs on my hard disc?
The security attribute of an item is stored as the object kMDItemSecurityMethod in the spotlight database.

This is usually a string. Until now I have found "none" and "Password encrypted" as possible strings. This doesn't mean necessarily that the file needs a password to be opened. It requires at least a password to be entered to allow a modification of the pdf.

So enter "Password encrypted" (without quotes) in the search box of your smart folder.