Yes it's possible.
And of course they will have different hashes, thats how you recognize the version from US/EU/JP/other
Use Offline List 0.7.3 beta2.
The dat (from Advanscene.org) contains duplicate informations.
Though, I don't know if you can exclude roms based on the region.
It's more a purpose to store them in the same archive, to gain space (while using 7zip, duplicates compress to 100% ratio, so having dupes or not result in the same disk space requirement).
There's a "duplicate filter" option which let you sort and exclude regions.