I see your point but for people who don't use many emu's it may be unsuitable to have say emu 1, 10 & 13 in use only.
Maybe layout creators could make a small textfile to go with their layouts to just explain which EMU? is which, eg:
emu1 = mame
emu2 = zsnes
emu3 = gens etc.
Then people who've downloaded it can quickly alter the filenames based on their setup.