In the case of the U-2 and the SR-71, the altitudes they operate at provide threat protection and more importantly, area coverage for ISR (intelligence, surveillance and reconnaissance) sensors. Going to 100,000 feet does not provide a significant intelligence benefit, nor does it provide greater threat protection.
Service ceilings can be overcome by providing different powerplants. ECS (environmental control) can be redesigned (if needed) to handle higher altitudes.
Edit #2: In the specific case of the SR-71, the thrust capabilities and the wing surface area limited the max sustained flight. Practically, that was just below about 85,000 feet. However in certain situations, altitudes above that were flown.
Edit #1: Above about 100,000 feet the atmospheric density drops off, which provides a practical limitation to airfoil and air breathing powerplant operation.
As I understand it, from working most of my career with SR-71, U-2 and satellite assets, the real issue is that there has not been established the need for aircraft to go higher, and therefore, there is no business case to develop aircraft to do so.the real issue is that there has not been established the need for aircraft to go higher, and therefore, there is no business case to develop aircraft to do so.