A lot of people have already asked for water bottles to stack and it's been shot down with the argument that "it would make it too easy".

Well, people can already config the mod to turn thirst off completely. Is that too easy?

Letting people choose if water bottles stack or not and to what number (1-64) with default value of 1 would keep everyone happy. In my opinion stacking would also make it consistent with the Minecraft rule of holding 64 pork chops in one hand.

If changing the number to which items can stack requires separate definitions I'd suggest just the default 1 and alternative 16.