The vents and return system would have been there since its manufacture.
I don't think they would have done that and not install that type furnace.
So, under the circumstances, I believe either it was changed within first 3 years or changed at beginning because someone didn't want that type system.
Whoever installed what is there now, would have known to cut the doors.
With that said, there wouldn't be two return set-ups. So, if you have a return grille at the closet door and a filter in furnace door and air is being drawn through there, that is a return system.
With that info plus the fact that the air at those vents is blowing out, not drawing back into belly, that return system is not operational.
Now, I'm not there, but with the info you've given, I'd say it is ok to seal them up.
Take care and best wishes,