I have clear tempered glass on my cocktail. That would probably be best if you are going to have a graphic underlay, the smoked glass will probably mute the colors on the graphic a little. I have an instruction card under the smoked plexi on my upright, and it is a little difficult to read.
If you aren't planning on a graphic underlay, then I would say go with smoked glass. It just makes the screen look better, IMO. If I had it to do over again, I would use smoked glass on my cocktail since I don't have any graphics under the glass.