Over the years I have developed a specific way to store empty supers, but your method may differ. A lot depends on how many supers you need to store and the amount of storage space you have. Another issue is pests. Mice and wax moths can be especially hard on stored equipment.
I keep empty bee boxes—with or without drawn comb—in stacks in an enclosed shed. I crisscross the boxes so that each box is at a 90-degree angle to the one below it. This allows the free flow of light and air throughout the stack.
Light repels wax moths, not mice
Wax moths do not like light, so a stack with lots of light inside is a good thing. I should mention that my shed (which is really my garden shed) has both windows and skylights. I know this seems like prime real estate to waste on bee boxes, but I don’t use the space much in the winter anyway.
However, it is not a perfect system. Mice don’t seem to mind the light and one year I had mice make nests right in the drawn combs. They made creative use of chicken feathers, woodchips, peat moss, and straw they found in the area. Once they were comfy, the mice munched on the combs that contained honey and pollen.
So now I stack the boxes and place mouse traps on all four sides of each column and I add a few extra inside the stack on the floor (you can buy them in bulk). It’s worked so far.
Mold likes damp frames
The “open stacking” method also inhibits mold growth. One year I stored a few supers that had honey and pollen in them and, in order to keep mice away, I closed up the stack. By spring, the combs smelled moldy and disgusting.
Since that time, whenever I have frames with honey or pollen, I give them to an overwintering colony. The bees manage to discourage mice, moths, and mold better than I can, so I let them.
Use closed stacks if you are treating for wax moths
Beekeepers who must treat their empties for wax moths often stack the supers in line with each other so no light and air can enter. Inside these closed-off stacks, they place insecticide to kill the wax moths.
Of course, insecticide-treated frames and boxes must be totally and completely aired out in the spring before they can safely be used on bee hives. It’s another step you need to do before a nectar flow and one you must not forget.
Your empty supers are unique
So again, it depends on your situation. I don’t use pesticides and I’ve managed to keep wax moths at bay by always freezing my honeycombs after harvest and by stacking the empties as I’ve described.
I’ve seen people just stack their supers outside, but around here rain is a problem as well as lots of wildlife—including mammals, birds, and all types of invertebrates (bugs and slugs)—so I keep them inside.
As with anything else in beekeeping, you may have to try a couple of different methods to find out what works in your area. It’s all part of learning the ropes.