Storing a car with the suspension hanging can damage the control arm bushings because they are strained in torsion. For winter storage just change the oil/filter, fill the fuel tank and keep the battery charged either in the car or remove it. Pump the tires up to 40 psi.
Nylon belted tires will tend to flat spot when cold, but they go round again once the tires warm up from some driving.
I've been storing cars for 6-12 month intervals for the last ten years and have never had a problem with permanent flat spotting.