I have tried two diffeent paints for this purpose.
You can use two-component epoxy based paint. This paint is somewhat expensive but I almost guarantee you that it will do the job right.
Epoxy paint is often used by fish ethusiasts in Norway when they make wooden aquariums.
Just don't mix more of the paint/hardener than you intend to use in one session.
I used clear epoxy paint for a small mourning gecko tank I built once.
When I put on the last (3rd) coat I first put old leafs on the sides of the tank. When I painted over the leafs the paint soaked through and the leafs were sealed in the paint.
Nice effect to a tank.
The second paint that I have used for this purpose is called "paintable bathroom membrane". This paint is used in bathrooms on all surfaces prior to putting on tiles. It is a rubber based paint and when applied as instructed it will give you a 2 millimeter thick rubber membrane that is said to be 100% waterproof.
I used this paint for my new 250 gal giantgecko enclosure prior to putting on the cork boards. I apllied double thickness to the bottom just in case.
Unfortunately this paint is also kinda expensive.
Another thing you might concider is a rubber pond membrane. This is a black 1-2millimeter thick ultra tough rubber membrane that is used in outdoor ponds. Just glue to the sides with silicone and seal the corners, also with silicone. I haven't tried out this but I believe that it will work good also.
I you descide to use silicone you can use thinner (concentrated vinegar if you use a vinegar based silicone) to thin out the silicone enough so that you can paint the silicone with a brush.
Regards
obeligz