in college I drilled several bottles and glass items. I was using a rock / masonry bit that I was using to drill rocks at the time. This worked quite well, the only issue being at the final cut through, these are rough bits and they would try to rip the last chuck out and this sometimes killed the bottle. If a larger bit is used & you'll need a file in order to get the downstem to go the correct direction

Oh, BTW, smoking out of bottles generally sucked, I'd make aa hooka out of the bottle, it'd work better. good luck!