I will agree that Native American Spirituality was the first form(s) of religion in what is today the USA...however it was not what the USA was founded on. Which, to answer your question, is why there is not a Payote plant in front of every court house. But to be honest if our Constitution and laws were based of Native American Spirituality and the Payote plant was used to symbolize the laws roots in it, I would not care at all.
If a judge basis a ruling on the basis of his or her own personal religous beliefs, that is not seperating Church and State. However as long as Judge Roy Moore can rule from the bench with an open mind and by the rule of law, and not from his Christian beliefs what harm is being done by displaying the 10 Commandments to reflect our laws basis in them? What should that matter on your case before him if he is not using it against you or to judge against you?