Help with frog vivarium?

Yes, the soil can mold, so either fix the silicon or be prepared to replace the soil more often than you would normally need to. Since you keep water in half the tank you need to periodically check the glass, soil, and any plants you have for mold anyway, so the soil being constantly damp will only add more work and cost for you. If you end up finding it's doing a much better job at keeping the humidity up than hand misting you may either want to leave the setup as is or consider fixing it and adding an automatic mister. Both solutions will make you have to clean more because the higher the humidity in the tank the faster mold will grow.