maybe the Due's shield input pins will all be '5 volt tolerent'
I wouldn't bet on it, the SAM is in no way 5v tolerant (4v on a good day) so that would need extra circuitry, possible but not obvious from the photos and I can't see them adding 54 level converters or even 54 current-limiting resistors.
I think the Due will drive most shields (voltage wise, maybe not with current) and if not then no real harm done unless too much current is needed from IO pins, but any shield that returns 5v (probably just about all of them) has a good chance of shafting the SAM3. That will be a very expensive plug in and impossible for the average user to fix.
I will also be interested to see how this all works out.
Rob