Do Skunks Dig Up Potted Plants?

I would hesitate to place mothballs where animals can get to them as they are very poisonous to them.

Yes, they will dig, dig, dig for anything that smells like food as some plant fertilizers. A few moth balls on top of the soil will discourage them. Skunks do not have good vision, and they hunt food by scent. Some fertilizers contain blood meal and this may what is attracting them. Skunks will dig out all the grubs they find so they can be beneficial if you don't mind little holes. If the plants are completely torn out, that may be young raccoons; they are quite destructive.