This PAUSE that you refer to is common with youngsters at that age. Kids are learning something new everytime they step onto the infield, pick up the ball, and TRY and reach home plate. The surface that their pitching off of doesn't help matters any, and more often then not, their not as prepared as they should be ... and who can blame them... their nine (9).
As far as hurting themselves, I doubt it. Oh, you'll have some sore arms and elbows for sure, and that's a given at this age. Pitching itself is not a natural thing for the body to be doing anyway. So, the kids get a ball, tries and resemble something he/she saw on TV, and let's-it-fly! And by the sounds of it, that's what your experiencing now.
Th important thing is select kids that have a natural flow with THROWING the ball ... not forced. From this population, you have a pitching staff (rotation). And at that age, this is the best you can expect.
Moreover, keep a serious record of PITCH COUNTS. Don't let a kid stay in a game for sixty (60) pitches an inning.... for five inning. And from your question here... its sounds like you have a much better handle on the health of your charges then to allow that.
On this web site there is an information bar that runs along the top called ARTICLES. "click" on to that and scroll down the subjects till you come to an article titled "Pitch Counts". That article is very helpful for coaching youths.