i actually tried this when i first got my nanocube, as one fan was noisy (called and they told me it had bad bearing and sent me a new one). i didn't notice a temp change either way in the tank, but I think having one in and out helps the lamps themselves from overheating? i know the guy at oceanic told me this as well, and i'm guessing if your tank is still under warranty i'd leave it the way it came for now. my 29 biocube doesn't go above 78 with the one fan in/one fan out, and i even have a heater.
btw, if the fans get noisy, peel back the sticker and dab some vaseline on the bearings. it helps immensly! i've had so many issues with my biocube canopy: bad ballast, two bad fans, one of the screw holes broke on the plastic lamp cover, and the top doesn't fit right on the tank! i've only had it for 2-1/2 months!! but oceanic is going to send me a whole new top. they've been great with warranty, just sucks i need to use the warranty so much!