The answer: It’s not easy. Any material that is extremely hard (meaning glass, granite, concrete, etc.) cannot be precision drilled using a conventional pointed drill bit. Even a carbide or diamond tip drill bit has a limited capability and will create a lot of unsightly edge chipping.
Glass is one of the most difficult materials to drill because any defect in the hole or edges of the holes can be seen. Usually, with granite or concrete, the hole is covered up, but with glass, even if it’s covered up, you can still see a defect when looking through the glass at different angles.
Glass drilling machines are designed with drilling heads on both the top and bottom sides of the glass. Using high-quality diamond core drills on both sides of the glass prevents chipping of the glass. When the top and bottom drills almost meet in the center of the glass, the bottom drill retracts, and the top drill continues drilling and finishes the hole.
Check out this short video of how 2-3/8″ diameter holes are drilled in glass for mounting clock movements.