The way we drill holes in glass bottles is to use some Sculpey or Fimo (poly clay) and roll it into a rope. Make a circle of it and press it onto the glass, making a waterproof donut, you will drill in the center of this. Put water in the 'pool' and use a diamond bit.
You must use a steady hand, so we use a drill press and hold the glass still.
Just another way to do this :)