In principle, Paperpile should not create duplicates. If you see files with duplicate names the reason can be that you imported from sources like your hard-drive or Mendeley that contained duplicates. In that case Paperpile attaches all files it finds to one reference (as we don’t know which one you want to keep).
Also the use of some third party Google Drive sync programs may mess things up.
But in general if you want to clean up space going after your PDFs is typically not the most primising. Often there is a video file somewhere which is as big as your whole paper collection. But that’s just a personal experience, your situation could be different of course.