The wheels I've currently got on my daily that used to be on the on the project before I parked her up, I kept inside the house for a good year and a half. They started off in the under-stairs cupboard on their end as they held their pressure, and then they moved up into the spare room where I kept them stacked 2 tall. Needless to say keeping them in the house probably isn't ideal for most
The rest of my wheels that are worthy of use (The OEMs from my project lude and the Aerodeck) I have stacked in one of my sheds (literally 8 tall) The lude ones had been stacked 4 tall for probably about 2 years previously, and the addition of the 4 Aerodeck wheels has probably been for about 6 months (Since I've had a sort out.)
None of the wheels have shown any signs of perishing from simply being in a shed. I've not covered any of them as I feel they should be aloud to breathe. Stacking 8 tall probably isn't ideal, but the likelihood that I'll ever actually use them again is slim. The lude ones I'll just use for moving the lude around if I need to. The Aerodeck ones are on top and I'll only ever use those for the MOT.
I've seen people build a rack for wheels before, utilising 2 horizontal wooden beams to sit them in, but I always see that as a bad idea as simply sitting the wheels on two narrow edges can't be any good for a prolonged period of time. At least if they're laid flat, the weight is spread around the whole circumference. Or hang them on padded hooks from the rim themselves.