Why are the enclosures getting THAT cold in the first place? Regardless of what you do with the water bowls, you MUST get that issue fixed, or you will end up with some sick snakes on your hands.
Temps should stay around 80 degrees at ALL times...for ball pythons, at least. I'm not as familiar with minimal temps for boas, but I believe they are about the same. Absolutely no less than 75 degrees for the balls. Just because they have a warmer side of their enclosure doesn't mean they will use it, even if it's super cold. There have been studies that show snakes will wander out into freezing temperatures and die, even if they have a warm enclosure to return to. We should not expect them to "know better"....it's up to us to provide healthy temps.
As for the water bowl...if they're more inclined to soak and get even more chilled...then yes, remove the bowls at night. They don't NEED to soak anyhow, unless they're trying to relieve themselves of parasites.
But please...do whatever it takes to get those overall temps up...then you won't have to worry about the bowls at all, and your snakes will be far less likely to develop life-threatening RI's.