Here is an old compilation of questions I had in a file, obviously you can't ask all but pick and choose. I would also role play with your son and have him ask questions of you and or friends to become more confident and also work through the questions he feels important. Good Luck!
Questions for coaches
What kind of academic support does the college provide? (tutors, etc)
What is the team grade point average?
What is the team graduation rate?
What are some of the majors of team players?
What happens if I have a class and practice conflict?
What are your red-shirt procedures? Will I be red-shirted in my freshman year?
Does the scholarship cover summer school?
Will the scholarship cover a fifth year if necessary?
At my position, what does the depth chart look like?
Where do I stand on the recruiting list?
Have you seen me play? Where/when? How do I compare with others you have recruited in my position?
What are my scholarship opportunities?
How many assistant coaches are there?
How many freshman do you typically bring in, either as signees or as invited walk-ons, on average how many of them are still at your school 4 years later, and what are the normal reasons for leaving?
Are you happy with the University/administration? Are they supportive of the program and you?
Is the program fully funded? How many scholarships does the program have?
Ask specific questions regarding how much does scholarships change over the 4 years. What does a typical mid week starter get? A starting position player? A weekend pitcher?
Questions for Team Members
Does the coach teach at the school?
What is the morale of the team?
Does the team like the staff?
Is the coach interested in academics?
Do the athletes really have to go to all classes?
How long is practice?
Would you go to this school if you had to choose again?
What is the average class size?
What are the dorms like?
Are the professors accessible?
Do the athletic dept. tutors do a good job?
Pitching / Playing questions
Who is the pitching coach?
What is his pitching philosophy?
What is he looking for when recruiting a pitcher for the program?
What are the off season work outs?
How much rest does he want his pitchers to have in the off season?
Does he limit pitchers with pitch counts?
How many Freshmen pitchers pitch?
Are there any Freshmen starters?
How many Freshmen are redshirted?
Does the program recruit 2 way players?
Can a pitcher DH and pitch?
Are there any 2 way players on the roster?
Questions for Admissions
What is the average class size and ratio per professor?
Who teaches classes? (Professors, teacher assistants)
What is enrollment of college?
How is my major regarded?
What percent of graduates from my major receive jobs within three months of graduation?
How many fraternities and sororities are available?
What are the housing policies?
May I sit in on a class in my major? (as a guest)
How accessible are counselors to me?
Summary Question for Yourself
Did I have a good overall feeling about the school?
Would I go to school here if I wasn't going to play sports?
Will I fit into the athletic program?
Am I satisfied with the living arrangements?
Am I satisfied with the academic opportunities?