I have my honey supers as deep, never migrated yet to any other size. I like the deeps, kind of stuck on things I guess.
When I go to take the honey frames, I have an empty super alongside that hive. That empty deep sits inside a telescoping lid. No bees can get in (usually I will have this set up in a wheelbarrow). I take out a frame, bump the frame, many bees fall off, I brush off as many as I can, quickly and sharply, one must brush in this manner, or you just REALLY irritate the bees. I place this frame inside that empty super and put my cover cloth over it. I do this as many times as required. I then take the wheelbarrow up to the house.
This is an eloquent description of what I did for years. It's also a good method for topbar hives.
I'm gradually switching over to all mediums and use a modified triangle escape board. The supers are usually empty in a couple hours, but I leave them overnight and usually only need to brush off a few bees. I pull the supers in the early AM before there is much activity.