As far as I know, there's no such option in PL/SQL Developer. There is a plug-in called "Save separate" from "BAR Solutions" which is made for exactly that purpose but I'm not sure if it works (especially that it has not been updated for a long time (many PL/SQL Developer versions ago).
I also have to save spec./body pair in separate files at my work, but I found working on them separately (separate windows) quite convenient so the problem does not affect me so much.