Personally, I will replant or add a thick layer of organic soil to my plants so the chameleons can't come into contact with those perlite balls or any sticks of fertilizer the nursery might add into the soil. But after that the only thing I might do is keep topping off the soil every few months, since it gets compacted, some drains out of the bottom over time, and I use it as a refresher for the plant. Since I don't fertilize the plants in my cages it's a way to renew their food supply.
If you never let your cage dry out then yes, your soil will start to get disgusting and the plants will start to die. That's why you want to not mist so much that your cage is sopping wet all the time without a chance to dry out (this will be bad for the chameleon as well, not just the plant). If you do allow everything to dry between misting sessions you shouldn't have a problem with mold, fungi, or gnats.
