There is no logical reason to assume that the Revolution games can't be designed to support the Gamecube controller slots. There is EVERY logical reason, however, to assume game designers won't be doing that even if they can.
And before you say something like "well why go to the effort of letting designers use them if they won't", the reality is, I'm almost positive it would be the other way around. That is, they would have to go to the effort of BLOCKING those ports when in Revolution game mode.
"On two occasions, I have been asked [by members of Parliament], 'Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?' I am not able to rightly apprehend the kind of confusion of ideas that could provoke such a question." ~ Charles Babbage (1791-1871)