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?
I Normally just leave them as they are when i downloaded them and chuck them in a folder on my server which I can pull down on any device when I need them.
I have terrible but defined habits for my ROMs. I use the same folder structure for all of them.
./[platform]/[game]/[game].zip
./[platform]/[game]/[game].iso
./[platform]/[game]/saves/...
If it's a series, using Pokémon as an example, I also have:
./Pokemon/Backups/[game].zip
./Pokemon/[generation]/[game]/[game].iso
So it's not that good of a backup, mainly there in case the iso corrupts, but I think it's better than nothing.
Uncompressed playable format.
Backups are done with Veeam on a selfhosted Backup and Replication server
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.