Yes, the airframe does age.
But the skin and frames and bolts and rivets are inspected, and checked based on actual flight hours. Note that many, many Air Force planes have low flight hours/year compared to the civilian daily use in many flights. (This even with the nuclear alerts under SAC.)
But, the USAF B-52 used at low levels stress the airframe much more than the “gentle” turbulence at a commercial airline’s 35,000 ft. Almost all of those 52’s were retired. (B, C, D, F, G models.) Today’s are H’s.
The H models have benefitted from two things:
1) A strengthened airframe, significant modified from the earlier models, for low level penetration.
2) having spent the first half of their lives sitting ground alert, not racking upma whole heck of a lot of airframe fatigue hours.
Oh, 3rd thing too: since assuming conventional missions, the Hs operate at much higher altitudes than they were designed for (as you mentioned), further reducing airframe fatigue.