If you want waterproof, then silicone or epoxy are your only options. Clear silicone will work, but its hardly crystal clear...so while the base color of the paint will show through, lighter detail might get obstructed.
I posted on this subject in a similar thread just a few posts down. Epoxy will be the most durable solution by far, and is completely waterproof when applied correctly. You can find pseudo epoxies in spray cans and 1 stage paint on applications. These won't be as tough as a true 2 part epoxy, but should hold up pretty well.
What may I ask are you doing that you require it to be water proof? For a bearded dragon enclosure, almost any decent sealer will provide all the protection you need. Something like polycrylic or polyurethane will also hold up well to spot cleanings. I personally use Mod Podge, which is far from water proof, but its served me well for several years now. Mod Podge Hard Coat is water resistant enough that spot cleanings have little effect, and its so easy to apply (and non-toxic), that I can completely reseal a structure in a day should it need it. A truly water proof solution would be such a hassle to apply and maintain that its probably not worth the head ache...especially silicone. That would honestly look terrible. So unless you plan on completely submerging the item, pass on silicone.