But that's different. Water is not something that is discretely counted typically, but glasses of water are.

Unless you're the Mad Hatter, you'll be ordering a (whole) glass and enough water to fill it. We collapse the "glass of" into epsilon because it's assumed in polite conversation the waiter won't be pouring the water into your open hands.

There's nothing wrong with that. In that context, "a water" is the same as "a glass of water".