Why would short-haul flights be pressurised at a higher cabin pressure?
For the structural loading, the absolute cabin pressure is not as important as the pressure differential with respect to the outside pressure.

Short-haul flights typically operate at lower altitudes; either because they are operated by turboprop aircraft which have a lower service ceiling, or because there is simply not enough distance to climb to a high altitude and glide back to land. At lower altitudes, the outside air pressure is higher, and thus the cabin pressure can be higher without exceeding the maximum pressure differential the fuselage can handle.

Your other concerns are not really a factor. Only the pressurisation cycle count really matters to aluminium, not the total pressurised time duration. The fuel required for pressurising the aircraft is also not really a factor compared to the energy required to either heat or cool the air for passenger comfort.