taken from here [Tutorial] Installing rxTools Custom Firmware - (Old 3DS and 2DS)
@Tony_93 also the reason i thought you could play dsiware from emunand
Yeah, "reportedly" tells me that author has not tried it himself.
Anyways I think it has something to do with the way they are installed themselves.
All games and even GBA games have to be installed to the SD card, DSiware in the other hand are the only games that are installed to the NAND and have nothing to do with your SD, since emunand is located in your SD you really can't boot them from there.