When I click on a password protected pdf, DT asks for the password, which is reasonable.
But I would love it if there were a way it can remember the password for next time, and better yet if it could OCR and include the text of the pdf in search results.
One possible solution is to remove the password protection - the easiest way to do that is to open the PDF, enter the password and then print the PDF to DT. Instead of protecting individual files, my database is encrypted.
I open my PDF in PDF Expert and choose its command to edit the password (I choose a blank one). After that I can open it in DT without entering a password. I suppose other PDF apps can clear the password as well. (This is on my Mac.)