Exactly Brett. The lighter, more breathable nanoseeum does not handle really small gnats or other tiny bugs like the heavier stuff does. The two links I mentioned earlier make note of that in their comparison. For me, I'm mainly worried about mosquitoes and flies, both of which are no problem with the lighter nanoseeum.
Theoretically, it could be possible to put little holes in Cuben. Then again, the holes might grow and then you might not have bug protection. I'm not sure if the Dyneema/Spectra fibers which prevents the mylar from ripping are close enough to prevent the holes from getting too big. If not, you might be able to make a material like Brett suggests by simply removing the mylar from the Cuben.
I'm not sure if anyone is working on materials like this. It would be pretty much useless to the sailing crowd (the folks who gave us Cuben) and since it wouldn't be waterproof, a lot of the outdoor folks wouldn't be interested. A new waterproof breathable material sells really well, but a new material that is simply more breathable is a tougher sell (although it obviously has its place).