I've never heard that they typically poo in the water. They will often let loose if you soak them in a tub of water, but that's different than their own water dishes.

I personally, would NOT want to encourage such a behavior...because how long might it be before your roomie noticed how disgusting the water was and the snake would have only fouled water to drink?

Regardless though...they go where they want and I don't think there's a way to encourage them to do otherwise. Just make sure whoever is watching the animal knows how to care for it and is trustworthy.