Steves idea about making a "snorkel" sounds good to me.
I was actually thinking of doing the same on my Agility 50. I want to keep me scoot looking like its not been too modded but at the same time get more power/speed so thought of making some kind of intake and doing away with the stick rubber hose for the airbox that just kind of hangs there looking sh!t.
I was going to cut an intake hole somewhere on the front of the side panel, the colored panel under the seat, or in the front under my seat and planned to put a car bonnet vent or scoop of some kind over the hole. Then was going to run a wide hose of some kind into the airbox.
I bought a few intakes off ebay cheaply to try it but i have yet to find something im 100% happy with before i cut up my panels. Just resprayed my scooter a couple of months ago tho so now im wary to cut it up cos its looking nice right now. Probably look at it again when i get time to plan it out properly.
Same idea would work on your cvt cover ,in my opinion, maybe im wrong but i cant see why it wouldnt work? Also as Axy says if you put a hole, (exhaust) at the rear too then air should, in theory, run thro the inside of the cvt prettty well i think.
Or what about fitting a race fan on the variator? would these not help? Seen them in load of shops and ebay pretty cheap.