Around here, there are lots of two way players for the smaller schools, where they need every player they can get. At the bigger, more competitive schools with multiple future college players, not so much. My eldest SS/CF had the arm, but only pitched a handful of games as a reliever, and got to hate it, because it was usually in an emergency situation with little to no warning. He threw pretty hard for a non P(round 85), and his arm started to hurt, so it affected him in practice the next day, and beyond. He also hated seeing balls drop in the OF when he was pitching that he thought he could've gotten to. Another MIF friend in the same situation messed his arm up so bad he had trouble hitting, which was really bad because he was a bopper.
Once they get to be big boys, with the big boy velo, you can't be messing around. Proper warmup, and rest between starts is essential. If you are a starting P/SS then one out of every 4 games at a minimum you will be missing from the MIF, and chances are that will throw the D out of whack. If you are smart, you also should be resting your arm properly between starts, which might mean missing another start at SS. That REALLY messes up the D. To me, the only position that is semi- ok is 1B, as the stress on the arm is minimal. DH, of course, is fine.
Every year i see it. Dad's bragging about how their son can play both ways, and how he has a rubber arm. I used to do it. Here's the thing...they usually don't tell you about the pain till it's bad. They might whisper among themselves, but don't tell coaches, or parents. Next thing you know, the kid is in a sling, out for the season.
As far as colleges, I know this. Many coaches promise a kid that he will get a chance to be a two way. Very few coaches actually let a player be a two way. Exceptions are small colleges(usually HA D3's) that are not known for their baseball. They are usually desperate for anyone who can touch 80 and throw a strike. Those schools also play less games, so there is more time to rest.