Whenever the metal is heated the properties of metal varies as per temperature increase, but the mud vessel does not change its characteristics with rise in temperature. The change in characteristics in materials while heating changes the quality of food cooked. Moreover, the mud vessels has pores which makes the substance in mud vessel cooler comparing to atmospheric condition (ambient condition) like natural refrigerator. That is why the food is preserved for a long time comparing to metal vessel comparing to mud vessel.
There would need to be a double blind longitudinal medical study to determine any effects (both short and long term). No such medical study has been done, and I can't imagine one being done due to the cost, complexity, size, and length of the study needed.