I would have your son fill out every questionnaire, no matter what his level of interest.
My son filled out every questionnaire he received but one -- a college that was totally out-of-reach academically for him. In hindsight, I realize he should have filled that one out too. Who knows -- the coach, after seeing his GPA/test scores, could have passed his name onto another interested party.
You've probably heard the phrase, "Baseball is a small world," a million times. The saying really is true, and you never know which school your son's name might "trickle down" to.