Boxes help prevent stuff from banging against a carboy. It might not break immediately, but little cracks develop over time and it can fracture with little warning.
Covers are to keep light out of aging wine. I believe light causes taste and color change.
Of course some folks might just be really into tricking out their wine room, like putting spinning rims on cars. LOL
My wine sits in carboys in a closed closet, so I do not cover them. If for whatever reason, the carboy is going to sit out exposed to light. I tend to throw a blanket over it. I never leave them out like that for long though.
Given centipam's comment. I know over prolonged use. Many materials can begin to become more brittle. Does anyone rotate out old carboys for newer ones after a few years of use?
I believe that LOTS of light will affect wine in the LONG term, so I have curtains the I use to keep things dark in the winery. No need to worry about covers.
I love to gaze at my wine, so no covers. They reside on shelves by themselves, so hopefully I don't need the mechanical protection and use drag shades on the window.
That said, I now know what to do with my old "Ski Naked" tshirt::
A wine cellar is best without daylight since it is probably long term aging. I am not concerned about daylight on carboys. However I would be concerned about direct sunlight hitting them causing temperature fluctuations throughout the day and everyday.
I think the carboy covering started from some winemaking books indicating light exposure could cause damage. I agree with Dan and would certainly protect from strong sunlight. I found this link to some information from Enartis.