I wonder how hard it would be to custom cut a set of glass discs - maybe just a few favorite combos. Perhaps there would be better overall resolution (less distortion) than plastic gives?
I doubt that the material makes a significant difference, but the direct answer to the question is: not hard if you have the appropriate equipment, which is:
1. Drill press
2. Glass drilling bit
3. A shallow pan of water
4. A few 6"x6" (say) pieces of flat scrap glass, thickness 3-6mm ("base").
5. Safety equipment - good goggles.
The drilling bits look like small cylinders with a shaft. They are coated with diamond powder. I remember someone pointing to a commercial source on this forum.
Supposing that the colored glass you want to cut is thin - say, 1-3mm. You put the base plate in the pan, place the colored glass on top of it, fill the pan with water so it covers the top plate. Don the goggles. The rotation speed of the drill should be medium-low. It is "underwater" drilling. Press on the colored glass with a finger (precaution - you do it at your own responsibility), and drill through the glass until the bit reaches the base. Drill through, such that you fill that the colored plate has been drilled and the base has been just marked by the bit. Carefully knock the circle out of the bit. A new bit will be good for about 10 circles, I guess.
Warning - do not press hard on the drill, work gently. It works by abrasion of the glass by the diamond particles, nothing else. Do not stop in the middle.