First, congrats to your son for doing well in the classroom and agreeing to be challenged by honors classes.
You ask if by requiring this type of academic track you have hurt his options/chances for a baseball scholarship. Baseball scholarship monies are not tied to grades, although a college coach would probably think twice about giving any monies to someone with lower than a 3.0 GPA, as this type of student could struggle in college and penalize the team's scholarship allocation. The real question is, by taking honors classes, is he hurting his chances for an academic scholarship (on top of or instead of a baseball scholarship)?
I'm sure others can weigh in with much more info than I have, but here is what the NCAA says. As far as I know, these rules are still current:
In order for a baseball prospect to receive academic money and have it not count against the school's baseball scholarship allocation, the recipient must be ranked in the upper 10 percent of his high-school graduating class or achieve a core-course grade-point average of at least 3.500 (based on a maximum of 4.000) or a minimum ACT sum score of 105 or a minimum SAT score of 1200.
If your son can take honors courses and still achieve the aforementioned minimums, he should be okay.