I think that unless you can SEE evidence of mold, you don't really need to worry, and you can donate the boots. If the leather has organic-looking growth on it (green or white or black spots) then they either need to be cleaned or tossed. I would opt for cleaning and then if you're not going to wear them, donation, rather than just tossing them.
If you are concerned about mold growing in your shoes, or in your shoe closet, you can do several things. Give your shoes a day off after a day of wear, to let any perspiration that has accumulated inside them dry out; store them on a shoe rack or shelf or lined up on the floor so that they will air out (rather than in a pile). If you store shoes in plastic boxes (as I do) let them air out over night, before putting them back in the box. Canvas storage boxes are another option, although they are slightly more expensive than plastic.
Protect leather shoes and handbags from mildew and mold by cleaning with saddle soap, particularly at the end of the season or before storage. Suede shoes can be cleaned with suede cleaner, or can be taken to a professional for cleaning. Cloth shoes can be brushed and thoroughly aired before storage.
Normal wear, and proper storage, should NOT lead to moldy growths on your shoes, handbags, and clothes. If you ARE seeing mold on pieces in your closet, look carefully at the closet; you may have a leak that is causing dampness in the closet somewhere.