John,
A 40 mph pitch in the 9 year-old league is dangerous. The problem is not so much getting hit, but where a child gets hit. The problem is really not with the energy of impact but the fact that 9 year-olds do not have the reaction time to protect themselves.
This same situation occurred when my son was in the 9 year old league. He ended up in the hospital undergoing emergency surgery being hit in the mouth. He could not react quick enough to the inside fastball.
The danger is related, I think, to the reaction time, not just the impact.
Having said that, I think the major problem is that none of the other teams can get a hit off the kid.