well the MLB guys kyle Trains probably do use weighted balls. just because MLB Players do it it doesn't have to be best practice, there are also MLB pitchers who still run poles or Show up fat and untrained in spring Training.
the Training in MLB has probably improved in the last 15 years and there are now more Clubs applying sports science but there are probably still Clubs who do it because "if it was good enough for nolan ryan it is good enough for you" (basically we do it because we always did it).
I have myself asked questions if weighted balls are really having an effect or whether it is just the better conditioning that any decent program brings (causing kyles sensitive ego to explode
) but just because some or even many MLB Players don't do it this does not disprove that those methods are good. kyle has improved the velocity of many pitchers into the 90 and he wouldn't do it if he would not believe in it (but he also does tons of Training for the decelerators too so I would not just throw the heavy balls - although the load on the decelerators is actually lower with heavier balls because the arm Speed is lower and the decelerators don't kick in until the ball has been released).