CNC potentially can cut all materials, you're just very dependent on cooling and so on. And the router size is very important. I have a small cutting bed, made out of MDF.
This limits my options in what I can cut. Besides, glass is just too damn heavy and would be prone to chipping.
MDF would be a simple option, I might contemplate making a try-out set in MDF. However, I have to rebuild the cutting file every time. Different types of material require different cutting speeds and RPM's.
My main work on the CNC has been with Plexiglass so far. Maintaining clarity in plexiglass is damn simple too, just heat the cut edges ever so slightly. When it hits the right temperature it'll regain the clear-look. The only real downside is that the stuff is mighty expensive and it usually comes in plates. Every once in a while I visit the supplier to scavenge their leftover bin. I'll keep an eye out for a block of plexiglass. See if I can make at least one cup.
But like I said, all is in the designing-phase. The styrofoam cups were just me being impatient again. Main focus is adding functionality to the design. I've got some nifty ideas that I want to work out, but they all depend on the cups accommodating them. Then again, I might give the exterior design a make-over. I never quite know when inspiration hits.
Whatever you do, keep us posted...what you're up to is fascinating.