Recently I started making kits that require a whole lot of drilling. And by a lot I mean several hundred holes. So, I started with one tool and finished with a different one, I thought you might be interested in which tools and why. I made a little video for you about it (or scroll down for the text version).
Both a flex shaft tool (mine is not a name brand Dremel, but the premise is the same) and a drill press work well.
I like the flex shaft because it’s faster, I can drill more holes in less time. However, the vibration is really hard on my carpal tunnel, and my hands were very fatigued after not too long.
The drill press is slower, and I have a harder time gauging how much pressure is being applied to the glass so broke several pieces while drilling. However, it is much quieter, and has minimal vibration, which made for a slower but less painful experience.
So, my conclusion is: For one to a few holes, definitely the flex shaft dremel, for more than a few, the drill press is the way to go.