I use Yojimbo to file my PDF's but I though folks might be interested in a quick script to embed in hazel to automatically encrypt a PDF before Hazel files it for you...
http://www.scrubbs.me/my-notes-blog/2012/12/15/automatically-encrypting-pdfs-via-pdfpen-in-filing-workflow.
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set this_file to theFile
set pass_word to "password"
tell application "PDFpen"
open this_file
save document 1 encrypt using AES256 password pass_word
end tell