I feel proponents of evidence based medicine are perfectly aware of the enormity of the problem, and are working hard to improve the situation.
Our understanding of the human body has advanced enormously with the advent of modern science, but it is still far less complete than most people probably realize when they interact with doctors. Not to mention systemic issues (common to any technical discipline) where medical professionals have to effectively practice with a degree of faith because no one has time to actually review the literature underpinning any given consensus, and that occasionally breeds long lived orthodoxies which do more harm than good...