I am normally a proponent of larger gaps but in the case of hatchling colubrids I am a bit hesistant to recommend them, especially for hatchlings of some of the medium to small sized kingsnakes/milksnakes.
Without giving a specific answer, I have some general advice about building lidless hatchling racks:
1) Make sure the material you use is flat and of consistent thickness. MDF and melamine are usually the best.
2) Make sure your construction technique does not allow "racking" of the structure which can cause shelves to bend slightly.
3) Related to #2, make sure the rack is kept level so an uneven floor, for example, does not cause the rack to shift.
4) Believe it or not, the best thing to do is build the rack with slightly oversized gaps. Then use contact paper or something similar to slowly build up each level until you're happy with the results.
5) Boxes can have large inconsistencies in height and this has the biggest impact by far on how secure a hatchling rack is. You could have a rack CNC milled from a one ton chunk of aluminum and the box would be the weakest link when it comes to security. The upshot of all this is that you may have to have your boxes in a certain order and each space may have to be shimmed accordingly. Honestly if it were me and I was keeping small colubrids I would just pay the premium for something like the smaller polycarbonate boxes from Cambro. At least in the larger sizes they are the most consistent box I have seen.
6) Some boxes have tiny round "feet" on the bottom. Over time these boxes can sag slightly and the gap between the top and the shelf can increase. I avoid these designs for all racks now and would especially do so with a hatchling rack.
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Current snakes:
0.0.1 Gonyosoma oxycephala - Java locale (green)
0.2 Gonyosoma oxycephala - Malaysian locale (green)
1.2 Gonyosoma oxycephala - Java local (green)
2.2 Gonyosoma janseni - Seleyar locale (all black)
1.2 Gonyosoma janseni - Celebes locale (Black & Tan)