In case there's someone who's also thinking about PS3 ISO vs Folder:
Folders are good, but it has a massive amount of files and PS3 games in ISO files are much more convenient and compact to transfer from one place to another. I now kind of regret having all my PS3 game backups in folders because ISOs are just so much easier to work with.
If I end up reorganizing it, it'll take me a few weeks or a month, although well worth it as I'll then just drag and drop.