you can compile the emu with libwbfs. then you can just create a ISO with a shitload of roms on it by using the partition builder from wiiscrubber. then you can use the same technique that alt dol loading uses. it checks the fst of the ISO for all the files on it. the alt dol stuff filters out everything that doesn't end in ".dol" but you can change that to whatever you want.
the way emulators work, they just copy a file from the SD/USB to a buffer in memory and play it from there. so you just get the filesize and location of the rom from the fst and copy it into that buffer. even though it is possible, i still say it is a bunch of work and a waste of time for essentially the same thing as what can already be done. and you will need to use a cIOS that supports WBFS for this, rather than just a IOS with USB junk.