Do pharmacies always have some naturopathic medicines?

Yes. Naturopaths claim any product that is not developed through standard fda approved therapeutics as in their domain. The profitability of these products is not lost on pharmacies and most carry some of them. They usually do not carry the exotic ones however.
Proven vs unproven. By definition, "alternative" is different than modern western medicine. Generally any drug, herb, treatment, or procedure that stands up to rigorous scientific scrutiny is included in modern medicine. The problem is that many alternative practices, herbs etc do not stand up to scientific scrutiny and cannot be shown to work. They therefore remain "alternative". Be careful and watch your wallet.