I think they'll definitively appear on the card game. At the very least Chicchimon, as the number of Babies are very limited and they're already reapeating. But this makes me wonder if they'll acknowledge Chronomon's status as SU with a Lvl.7 card when his official line goes Perfect -> him. That always bugged me since that line got introduced. Of course, the card game could make a mechanic to allow Butenmon to evolve to Holy Mode, or use Destroyer Mode as the Lvl.6.
EDIT: Corrected the Lvl numbers.
He actually made appearances outside of the ds story games, in other ds digimon games and in those he was just a mega, not ultra.
Also milleiumon in rearise is ultra so him being lv7 does make sense, it seems the devs do see him as a more powerful than ultimates.
Also I see both DM and HM similar to rasenmon FM and the normal.