For indefinite storage, I keep the cardboard "feet" and the tissue paper underneath them in the shoes to maintain the shape. Just like if they're fresh from the store.
If they came factory laced I leave them like that (fun fact - the 2000 black Vs did NOT come laced).
I do NOT use plastic bags, silica packs, nor do I ever shrink wrap anything. I don't believe a highly excessive amount of moisture is a good thing, but I do believe the TOTAL constriction of nearly all oxygen and moisture will kill the materials quickly and probably prematurely cause them to crumble to dust upon re-exposure to the environment. Unless you're living in tropical Africa, I don't think the normal generally minuscule amount of moisture in the air is going to do a lot of harm to stored shoes in a closet.
For the shoes I wear, I generally don't re-stuff them with the stuffing materials. It's just too inconvenient when all I want to do is grab a pair from the closet and go. Besides, worn shoes crease. No way around it. As Agent Smith would say, "It is inevitable, Mr. Anderson."
It's true. For those who have been following this thread, "elementary school playground busted" shoes are an inevitability.