The recent version only supports the safe removal of iPhoto duplicates. We're working on the new major version of The Duplicate Finder, that will support safe removal for Photos app as well.
As a workaround you can scan Photos library for duplicated photos on a file level, but their removal might cause inconsistency in the library, so we highly recommend you to make a backup of the library before the process.
1. Open the Preferences of The Duplicate Finder then select "Under the Hood" and “Treat bundle content as regular files”
2. Add your Photos Library to the circle on the Startup Window (File / Add Folder or drag and drop will also work.
3. Check out the duplicates.
Note: To delete files directly from Photos Library you can turn off “Item selection warnings” in Preferences / Behavior. But use it very carefully. You can also allow this option for auto select. Make sure you have a backup of your Aperture Library, before the removal.