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There are none related programs to find duplicates of any files in specified folders using file hashes to detect the duplicates using programs like CZKAWKA_GUI. It can create hard/soft links to files if you want to keep files in specific folders which take up virtually no extra space.
It might also be worth looking at ROMSorter. TBH I don't know whether it will do anything useful because I have not used it.
going another step further the 1g1r project tries to create sets sans dupes, so some automation exists to help with that: https://github.com/andrebrait/1g1r-romset-generator or https://salumba.com/romlist/romlist_ui.php can assist there.