@simpleethat Well, my suggestion is to compress all of your roms into zip or 7z format (as the emulators support) for use on your Pi and to just store them in that format on your NAS. This way they are maximally usable on your Pi should you need to copy them back over.
The amount of extra compression you can get by compressing everything into giant 7z files is fairly small in most cases. There are some roms that can't really be compressed for use by emulators, mostly bin and ISOs. However, most of the emulators also support a compressed format for these types of file (chd, pbp, etc). All the time, effort, and electricity you spend compressing files to eek out a few GB of storage space just isn't worth it.