I think truly throwing over the top happens less than often thought.
Body lean often makes it appear that a pitchers arm angle is higher than it actually is.
Refer to this picture of 3 high school pitchers here (our school having a no-hit victory in state quarter finals :-)).
Look at the angle of there arm from the elbow, and they are barely even three-quarters. The 3 haven't had any pitching related arm problems to my knowledge. They are all in the 80's easily with the one on the right throwing a consistent 87 as a sophmore.
Also refer to this picture of Johan Santana, my favorite pitcher to watch and everybody will agree he's got some dirty stuff.
His actual arm angle is between three quarters and side arm, but his body lean allows him to have an effective release point.
Overall I'm not a big fan of teaching a specific arm slot, other than avoiding a whipping side arm motion, because from my experience overuse injuries such as tendonitis come much quicker for young kids from the sidearm slot.
I also think true sidearm can be especially detrimental to actual velocity thrown, I see this in my younger brother as well as a former teammate, from a lazy sidearm they throw around average with a bit above average movement, but when they focus on throwing more over the top, ending around a 3/4, they have a noticable amount of more pop on their fastball.