Since the cardboard NUC boxes are generally used for transport, I suspect that the "deep" size they typically are is just to be universal. When we've picked up a medium NUC 5-frame colony, the frames went into the deep cardboard box for the ride home and then were moved into woodenware at that end.
I do make wooden medium 5-frame boxes for our own use, but we have a couple of the cardboard boxes just for what I mention above.
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