You can run the AC with the top down on those 90 degree days just like you run the heat on those 40 degree mornings. Thats what I do. Top down all summer unless its raining. Drive everyday unless the snow is flying.
I can't remember where but within the last 5 yrs or so I read that HVAC systems in modern cars do not need to operate occasionally in order to preserve the integrity of the system. I don't remember why it was no longer the case.
You also need to run the heater to circulate the coolant through the engine block and heater core.
Failure to do so may result in premature heater core failure.