Whirlpools for public bathing and whirlpool baths for individual bathing carry with them many health and safety risks. The main problemn with public bathing is chlorine and bromine are not ideal elements to bathe in. State regulations usually require X amount of chlorine and bromine per number of bodies. (A better method would be measuring PH levels.)
Whirlpool bathtubs carry with them the greatest risk. Bacteria get trapped in the piped systems, then shoots into the tub when you turn it on (pretty gross, actually.)
Other reasons for experts discouraging hydrotherapy are the expense of wet rooms and misunderstanding of the the therapeutic value of hydrotherapy.