Yes, they can use either. I heard (on the radio) a game once (Texas vs ?) in which ONLY wooden bats were used. This was because one of the two teams had not gotten their insurance policy in place before game time, and did not want to run the risk of injury to the players. Aluminum bats, you see, drastically increase the speed of a batted ball. If the ball is hit back to the pitcher as a line drive, he rarely has time to protect himself, and can be seriously injured. Wooden bats, on the other hand, are "dead", meaning that they absorb a lot of the momentum of the pitched ball, so that the batted ball does not have as much speed.
But, from a practical standpoint, except for unusual situations like the one mentioned above, everyone almost always uses an aluminum bat. Because you get more power. Because they are lighter and easier to swing. And because everyone else is using them, and if you don't, you're putting yourself at a disadvantage.
So, if aluminum bats are dangerous, why does the NCAA allow players to use them?
College baseball suffers from an extreme lack of fans. In football, there's very little difference between the number of fans at the pro level and the college level, and in some cases, college teams have a bigger following than pro teams. In basketball, there's a little difference, with pro teams edging out college teams. But in baseball, the difference between pro and college fandom is HUGE. Major League stadiums hold 40-60,000 fans. The BIGGEST college stadiums seat less than 10,000, and most seat less than 2,000. Television? Every Major League Baseball game is available on SOME channel, but televised college games are few and far between. Even the College World Series is available only on ESPN2, the network that is "PROUD to bring you the X-Games". What a joke! Most college games can only be found on the radio. But even then, if your school's basketball team is still playing when baseball season starts, and a basketball game is being played at the same time as a baseball game, the sports network for your school will play the basketball game.
I don't know why College Baseball is so unpopular, because personally, I like college baseball more than pro (and a lot more than basketball at either level). But the point is, right or wrong, not many people enjoy watching, or listening to, college baseball.
But even among the limited fan base of college baseball, most fans enjoy offense a lot more than defense. These fans would be bored stiff by a shut-out, and would put a bullet in their brains if they had to endure a no-hitter. They want to see RUNS, particularly HOME RUNS! And the NCAA recognizes this. So they allow aluminum bats, which give a huge advantage to the batters, resulting in more offense, and MORE HOME RUNS! If they didn't, college baseball fandom would shrink to the point that women's tennis would be more popular.
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Absolutely not! If they used aluminum bats, Mike Stanton would be hitting 600 foot home runs on a consistent basis, and anyone hit by a batted ball would get seriously hurt.