Your son can also ask HS coach for a letter of reccomendation. Most coaches will gladly do this when asked and now is a good time to ask, when they are not so busy in season. What he has to say about you is far more important than what you have to say about him.
I would make it a practice to always treat your coach with respect as far as questionnaires go. I would think that most college coaches that talk to your HS coach, are mainly trying to verify the information you have listed on your questionnaire and to find out what kind of person you are.
The baseball world is a close knit group. Don't lie, just be honest, because they will find out. In fact it is a college recruiters job to "crosscheck" you with many sources, including your HS coach.
If there is not a box on the questionnaire for travel ball, or club team coach, do the same thing and ask for a letter (brief) from your travel or club team coach to send along with questionnaire.