While fur mites can be more challenging, for ear mites I've always had good results from using oil: almond, olive, mineral, or sweet oil all work. Just drip a little in each ear, then massage it gently and thoroughly, getting it down into the ear where the mites will hide. The oil suffocates the mites. The rabbit will shake its head and scratch and will eventually remove the dead mites itself that way. Many of the "natural" treatments are basically expensive oil.
I don't treat rabbits that aren't showing evidence of mites; they're not super contagious in my experience, and some rabbits just seem more susceptible than others (you might consider keeping the less susceptible individuals as your breeding stock). I don't treat the cages, other than to make sure they're clean and free of bedding that could harbor mites or other parasites; I prefer all-wire cages for that reason.