It really isn't a big deal if you don't plan to keep the bindings for more than a year or two. Skis can be wiped down, even ground and filed if a little rust forms. Salt and grime from road spray getting inside the bindings worries many people more. I actually prefer the box because I worry about theft. If someone has to bust open the box just to see if there is anything worth stealing that makes me more relaxed while skiing with 2-3 other pairs at the car in the ski area lot (or any parking lot). I worry some about salt damage with top racks, especially to bindings. But, it is the ability to bring more than one pair of skis without having them in the car or still on the roof in plain sight while I'm skiing or using a rest stop bathroom that makes a box attractive to me.
I would like a box for the sole reason of keeping my gear out of sight. When I bring more than one set of skis to the resort I don't feel comfortable leaving anything on my rack so I toss them inside the car. Sometimes they're still visible through the windows though. I'm not a thief so I can't say for sure, but it seems as if it would take a higher level of commitment to break into the cabin of a car than to pry open a rack. A box would solve that problem but when I think of spending the money for a box I go and buy end-of-season skis instead (Pon2oons on their way now, wahoo!).