There are some health problems that can be indicated by drinking a lot of water. You could check with your vet on this. That said, this sounds more like he's just learned if he wants water he can cry until you give it to him. I would try to go a few nights without giving him water- as hard as that is- and see if he will stop crying after awhile.
I don't personally recommend putting water bowls in crates, and actually recommend just a pad/little bed, maybe a blanket, and sometimes not even any toys in a dog's crate at night. During the daytime is a little different, but at night a puppy will wake up and make all kinds of racket if there's a bowl with them the in crate.