I will use what ever color you would like that's available but a couple of things you might want to consider. Performance wise, color doesn't matter but as a bowyer, I want to see what is under that glass. If there is a flaw in a lamination or a dry layup without enough epoxy, under clear glass it will show up. Use opaque glass and you and I will never know. Makes you wonder why clear glass isn't an option with some bows and an extra charge in others.
Clear glass is also less reflective than opaque glass from a camo perspective.
No matter how flat the finish, oils from your hands or a little string wax and the shine comes through. Clear glass will still shine to some extent but absorbs most of the light. Many details go into a bow design that either makes the bow shoot well or appealing to the eye. Without going into great detail, here are some of the things that effects how a bow shoots. The grip must be shaped in such a way to put the center of pressure in line with the arrow and in relation with the bows center.