It's difficult to ensure our bees have enough honey for winter, because in the fall we don't know if the coming winter will be the worst-case scenario or the best-case scenario. What does the worst-case look like? It can take different forms. If winter is warm, then the bees will be active all the time, constantly nibbling and depleting their food stores quickly. If it's frigid, the bees actually won't eat as much as in warm weather, but may be so cold they can't shuffle over to the next frame of honey to get a bite. The best-case scenario is a winter that's steadily cold but not frigid, with periodic single days when the bees can fly out and empty their intestines. This weather pattern keeps them pretty dormant, not eating much until after the winter solstice when brood rearing begins and the colony's activity level increases.

Some people keep each colony in a single deep for winter, possibly in a climate-controlled building. Some people keep their bees in a single deep plus a single medium. But most folks who keep bees outdoors in the north use two deep brood boxes and find that the bees make it through the winter just fine in most years
For most of us, a hive would be two deep brood boxes plus a medium super. It certainly seems like an easy remedy for those midwinter worries about your bees, right? Of course, the queen excluder would have to be removed so the queen won't be trapped down away from her bees as the cluster rises. But other than that, what could go wrong? Is this just prudent insurance to keep our bees from starving? Or could there be downsides to leaving a super on your hive?
In a tall stack, the cluster morphs from a ball shape into a tall narrow egg shape and eats its way too quickly to the top. They leave honey all around the emptied path they make as they rise to the inner cover. Beekeepers call this chimneying up, since the cluster is following the rising heat they generate up to the top of the hive. If they chimney up, it is often challenging for them to move downward again to access more of their food, and they may starve at the top even though honey is available below. Starvation in the presence of honey happens more often with smaller clusters; large clusters can usually move around better inside the hive when it's cold. But any colony can die if they are trapped in a tight cluster far from their last remaining honey stores.
Sometimes in the fall you'll find a two-box hive that feels quite light when you tip it up to gauge the weight. Then when it's opened, you'll see that all the bees and honey are just in the top deep. For a hive like this, it can work well to add a deep or medium of honey on top of the stack. The added box of honey will provide insurance. You can remove the unused bottom box, or just leave that empty deep at the bottom as a buffer area against wind at the entrance. The bees won't be starting in the empty bottom box, and so won't show the same chimneying effect that can happen in a tall hive with honey in each box
If you peek in during winter and see bees at the inner cover hole, the cluster has risen to the top. You can take off both covers and add solid feed above them (in the form of a box of honey frames from a dead hive, or an empty super shielding a pile of winter patties, or a shim around some sugar bricks, or fondant patties). Depending on the weather, you may be able to set the bee-filled box aside with a cover on top and rearrange the remaining frames of honey they bypassed from the lower box. Group those honey frames together and put that box above the box with the bees in it. Take care not to change the arrangement of the bee cluster. These emergency feeding maneuvers are a shocking idea to new beekeepers, but bees starving is much worse than bees having cold air touch the outside of their cluster for 1-2 minutes. The bees on the outside of the cluster will cycle into the middle to warm up, and the bees on the inside will stay warm and cozy, sheltered by their sisters on the outer layers.

Another downside to adding an extra super is finding either brood, or crystallized leftover honey in the super in spring. Each bee raised in a cell leaves cocoon remnants and a thin residue of feces behind as it climbs from the cell. This is why brood comb becomes darker and darker. Most beekeepers prefer pale comb that has never had brood in it for their honey. (Such comb is also less attractive to wax moths, since the protein that builds up in the walls of brood combs make that wax more nutritious for the young moths than wax that is used exclusively for honey storage.) In springtime you'll want to use that super as a super, so it would be best if it didn't have developing brood in it.
One easy strategy is to smoke the super thoroughly. This will drive all the bees (including the queen) down into the deeps. Now install a queen excluder below the super. The brood in that super will all turn into bees within about three weeks, and the queen will be unable to get up to lay any more eggs.Eventually, the bees will start storing nectar in the frames of the super, and things will be back to normal. (It's not a bad idea to confirm that the queen is below the excluder partway through this process, so you don"t return in three weeks to discover that she stayed up in the super and has been fighting to find room for eggs between cells filled with nectar.)
We know a local beekeeper who keeps each colony in a deep over a medium year-round. He says the queen really only needs the territory of one deep to lay eggs steadily and never run out of space, since bees are constantly emerging and providing empty cells for her again. The bees still have some room for honey in the brood chamber of one medium and one deep, and the excess goes above them in the supers, instead of bees filling a second deep brood box with honey before they start on the supers. He likes this system because the medium is on the bottom and generally the queen will be found in the deep. So he only needs to look at a maximum of 10 deep frames if he wants to find his queen, not 20 deep frames as most of us would.

The moral of the story is that many things can work, but you need to understand the consequences of your hive set-up, especially in winter. It's not unreasonable to play it safe and keep more honey on the hive going into winter, but be ready to add solid feed if your bees chimney up. Be ready to chase brood out of the winter super if the queen starts laying in it, and don't assume that your bees need more honey than they've got. Two deeps full of honey should be plenty for most bees in most regions during most winters.