Most people deal with the 3-hour set playing as if they were forced to do that.
Musicians and a lot of people will agree with this.
My university has a band with which I've played gigs with less than 24 hours apart around here, and the night between both shows, I barely slept and was very tired during the second day. Even during the small rehearsal we had before the second show, I was still considerably tired. However, when the group that played before us finished and it was our turn, just listening to the "roar" of the audience (which was a local festival with around 1000 people haha), the adrenaline just fills you up entirely, completely, and you get focused and what you're doing, but most importantly: you have fun.
Because it's something you love. And now, these 1000 people were not there exclusively to see us, they were probably waiting for another group that was to play before us or after. Anyway, that was enough to cause a giant adrenaline rush that just keeps you moving. I wanted to play more until I ran out of repertory (And I'm not really good at all!)
Now, I can just imagine how is it to have WAAAY more people that that EVERY NIGHT at DIFFERENT PLACES IN THE WORLD to see YOU, just YOU. Man, I think it's like being the king of the world.
So no, I doubt the 3 hours long shows are an issue.
I think the main problem is traveling, most people got troubles to catch sleep while traveling, especially at planes. The time changes, you might sleep at 8 P.M. regularly but when you get overseas it might be 3 A.M. so you got to sleep earlier and that's normally not possible to do in less than a day. My thoughts.
Now, if age is another issue, I wouldn't mind Rudess having to sit during the gig to play, I'm not there to see him spinning around tho.
And for drummers, there is a TECHNIQUE, most non-drummers get tired after less than a short song of playing (Petrucci himself), and others endure much much longer, it's just matter of getting used to it, and this band, being better than the average group, has definitely mastered that.