how do you drill holes through bullet-proof glass?

Bullet-proof glass can be drilled with the same drill bits used to drill through regular glass. The reason why bullet-proof glass are is because it's a laminate, or sandwich, of glass and polycarbonate, which is an extremely tough plastic, and can already withstand bullets by itself if thick enough. But the combination is just that much more effective. The hardness of the glass shatters or at least damages the bullet projectile, and the "grab" stickiness of the polycarbonate finishes the job more easily with such a roughed-up bullet projectile.

The glass for bullet-proof glass is most likely a standard glass. When fabricating the glass, it has it's normal properties, where glass can be drilled. After the glass is cut and the proper holes drilled, it will then go through another process where it will make the glass "bullet-proof". I am not sure what type of lamination or strengthening processes this goes through, but I am positive that the holes are drilled before it reaches this process.

I believe that they use diamond tipped drill bits, or else the glass is formed with the holes in it from the mold.

Use a rotating tool to slowly grind a hole through it. It can resist a powerful impact, but you can grind it down slowly, using diamond drills or hard abrasives..