The muscles that are involved with acceleration and the muscles that handle the deceleration of the arm are different and complementary sets.
The purpose of weighted ball training is to strengthen the deceleration muscles. This is a sound approach to arm health, as many arm breakdowns are actually incurred from lack of deceleration conditioning.
When a player is building velocity -- whether just through improving mechanics or by growth in size or strength -- keeping pace with decel conditioning is a very good idea. I have no objection to weighted balls for this purpose, though I prefer using elastic bands of the sort favored by LPT's.
But don't confuse this with any thought that the weighted ball contributes to the velocity gain. It doesn't. Actually, the arm moves slower when carrying greater weight, so in this workout you would actually be working on throwing slower. Especially when you consider that true velocity gain requires that the arm stroke be completely in synch with hip and trunk rotation and whip crack. If you slow the arm down, you'd have to slow every other phase of the delivery down too, just to say in synch. Then you'd have to ramp it up again later.
That's too complicated and it doesn't work. Which is why weighted balls should be used, if used at all, only for their intended purpose, which again is to train the decel muscles so as to protect the arm from added velocity, and not to add velocity in and of itself.