I use emulators that play directly from (.iso) or (.img) files, however as you probably know, most ROMs are downloaded as archives.
Do you backup your ROMs in their downloaded archived format? Or as uncompressed files?
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I would have thought that the vast majority of people who download ROMs download them individually based off of their preference, not downloading the entirety of the PS1 or PS2 library.
To answer your question, it doesn’t matter other than compression. Backups are backups.