Hi blunayelf
I don’t have an answer for your question but curious as to which systems/roms use folders within a zip? Is this how they have been downloaded? In my experience, I have used zips in the past but due to having plenty of storage now, have gone back to individual files (a26, lnx, jag, etc). The only cores I use zips with are for arcade (fbneo and mame). Multiple files (ps1, ps2, dreamcast, etc) can be merged into one file using chdman.
How are you scanning these files? Automatic using a database (in my case, can be problematic) or manually, by selecting each option.