What we found out was as long as our son was academically qualified, the coaches at the D3's that he applied to made sure that he was accepted and that his application got a "good" look when they made acdemic scholarship decisions.
We generally knew by reviewing information from various sources (example: collegeboard.org)if he was academically qualified. In some instances he was in the lower 25% when viewing GPA's or test scores, but that is where having the baseball program as an advocate can really help.
If your son really wants to go to a particular D3 school, he should make and appointment with the admissions department for a personal interview. If he tells them of his sincere interest, it goes a long way in their decision making process.