How much moisture will the substrate need to hold? Will it be damp at all times?
I assume you want a solid color since you specify paint, so I'll limit choices those types of choices. I will list them in what I believe to be most water resistant to least water resistant.
1) Solvent based epoxy paints. Very expensive but you can seal a plywood box with these and they will hold water for years. Commonly used by aquarists to build large wooden tanks. Are very smelly and messy to work with as well as sensitive to improper mixing.
2) Water based epoxy paints. Still expensive, but generally easier to work with than their solvent based counterparts. Also sensitive to improper mixing.
3) Drylok latex based masonry paint. Remarkably water resistant for being so cheap and easy to work with. However, it is a hydraulic cement based paint and has a sandy texture to it. I would strongly recommend an easy to clean plastic floor of some sort is used in conjuction with this. Probably not the most attractive color, although it can be tinted. It sticks to melamine so it should stick to MDF. A bonding agent on the MDF might be a good idea to insure adhesion.
4) Some of the higher quality acrylic paints available. There is one from Sherwin Williams in particular that is highly regarded. Don't just get any old acrylic latex paint from Home Depot. One problem with these is that they are a bit brittle so they may not work with any thin panels of MDF than can flex. These also will not work with constant exposure to damp substrate. With these you should line the floors and first few inches of walls with plastic. I recommend scrap linoleum, vinyl film, or expanded PVC sign board.
One last suggestion I'll make is vinyl film used in the graphics industry. You can just peel and stick it right on the walls and floor. It is cheap but only when purchased in bulk so it may depend on how many cages you made. It is also very glossy looking.
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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)