The argument for using different bats in high school and the major leagues is primarily cost: wooden bats break when a fastball is hit too low on the bat.
But aside from skewing results for players - balls that would go nowhere due to a broken bat can be a hit using metal or composite bats - there is also a safety issue. For young players on defense, the ball can move much faster, because non-wood bats transfer energy to the ball better, a phenomenon called the "trampoline effect."
That makes the ball more dangerous. Such concerns have led to uniform bat regulations in college and high school baseball, but amid uncertainty about how non-wood bats perform in the hands of younger players, the rules are less consistent for that age group.