I would like to have duplicated photos stored in a separate folder, without clogging up the main library.

YES! PLEASE!

Since the folders represent albums, and I can justify having photos in multiple albums, detect duplicates and create symbolic links or hardlinks instead of downloading the file into multiple folders. This would reduce disk space used, as only one actually copy of the data has to exist while it can appear in multiple places on the disk. And it's never truly deleted until all copies are deleted from disk. This would work on NTFS partitions in Windows. (It also works on Linux and Mac filesystems, but CopyTrans is only available on Windows.)