Install qpdf from software center or http://qpdf.sourceforge.net
Open terminal in the folder where all your pdf files are located, type & replace your passwords:
mkdir -p temp && for f in *.pdf ; do qpdf --password=REPLACEHERE --decrypt "$f" "temp/$f"; done && mv temp/* . && rm -rf temp
Viola, now when you open those pdf files, no more annoying popups for password :)
Tested on Linux Mint XFCE
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