I've had a car on jack stands for up to two years. Not a single issue. If anything the suspension may start to sag a bit but I highly doubt it.

I store mine on wheel dollies for the winter, they're angled for the tire plus you can nicely tuck the car away into the corner of the garage since its on casters.

I ended up with these:
Auto Dolly M998027 - Auto Dolly Car Dollies - Overview - SummitRacing.com

why roll down the windows?

Humidity. Griotsgarage.com sells humidity eaters.

My car is on flatstoppers, battery manager, and full tank of gas during hibernation. No need for humidity eaters in my garage as there is no sun light to cycle hot/cold to induce condensation.

Condensation can also come up through the concrete during temp changes inside the garage, I throw a tarp under the Z when its stored for the winter.