What do you mean NES ROMs ending in .NDS? If you're just trying to load the NES games as NDS files, it's no wonder it won't work. What you want is
this program (download
here). Boot this application on your AceKard, then load the ROMs using it. You shouldn't have to do anything else as your AceKard supports auto DLDI patching.
Also, as far as Genesis goes I'd recommend
jenesisDS. amd for SNES I'd recommend
snemulDS. Keep in mind that neither are perfect yet, but they both support quite a lot of games.