It depends on many factors, among which is the size of the water bowl you'll use, what it's made from and how close you place it to the heat source. The humidity in the room where the rack will be kept also matters.
The upshot of this is only you can figure out what's best for your situation. Holes can always be added or can always be covered with tape. So don't worry about it too much.
Also, understand that the gap between the top of the box and upper shelf will usually provide more ventilation that you'd ever want to drill in your boxes, unless it's a VERY tight gap. Even if it were as little as 1/16" space that's almost 5 square inches of ventilation. That's about 400 holes drilled with a typical 1/8" bit.
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Current snakes:
0.0.1 Gonyosoma oxycephala - Java locale (green)
1.2 Gonyosoma oxycephala - Jave local (green)
2.2 Gonyosoma janseni - Seleyar locale (all black)
1.2 Gonyosoma janseni - Celebes locale (Black & Tan)