Diamond bits are the best to use to drill glass. As already stated you need to keep them cool. Using a water drip kit would be a good method. Or you could use a spray bottle, but this method requires an extra hand. Let the bit do the work never apply to much pressure.
Interesting idea I would like to hear how this turns out. What type of glass is this? The softer the glass the more resonance you should have.
I know this is a silly question, but can you build it without cutting the glass? You said just the top is glass. If its anything like the Cohibas I've worked with, you don't need to drill the top unless you're running a mag pup through or cutting a sound hole. If you're talking about drilling for a sound hole, have you thought about building a "sound port" on the side?
Would torching and melting the glass work? When it becomes viscous push a dowel or something through it? Just a thought. How bout a regular glass cutter?