You're right, metal fatigue is definitely an issue in airframe maintenance. The wings are designed to flex like that. If they weren't they'd snap right off. I don't know what they do now but when I was in the Navy they periodically took aircraft in for what was an x-ray of the entire airframe to look for cracking and other signs of metal fatigue. There is also a LOT of weight in the wings most folks aren't aware of as all the available inner space is used for fuel storage. In the B-52 it was surprisingly vivid just how much those suckers flexed just because the wings are so damn long.

The tire blow-outs on landing were the really scary part. Even from 1/4 mile or more away it sounded like a bomb exploded. I guess that was pretty routine. I sure saw a lot of em do it.