The only possible reason it could work is by increasing humidity in the oven cavity, and to do so in any significant amount, the water would have to be brought to a boil. Even so, there is no reason to believe that increased humidity would have any effect on the crust.
Otherwise, the only affect of the water is to provide an additional mass in the oven that will absorb the microwaves in competition with the pizza, essentially slowing down the heating process. It is conceivable that this might make it easier not to heat the pizza to the "rubbery crust" phase, but then the same effect could be achieved simply by lowering the power setting.
So no, there is no scientific basis for this belief other than the placebo affect.
Reheating pizza is one of the most challenging tasks, and there are many methods, none ideal.