Genesis (and SNES) roms can be multiple files, but the most common emulators use merged 'blob' formats, ie all the data from the cart joined up into one file with a header attached.
MESS (or UME) which are MAME based, but modified to run console/computer software as well, use 'correct' rom dumps where available, multiple files or single files. Typically a MESS/UME set won't be fully compatible with other emulators for that reason, but is more correct in terms of representing what was in the cartridges.