KauaiDad,
I agree with justbaseball and BOF. We found a number of coaches who were straight with us, a few that didn't know what to think or do, and a few programs that welcomed him with open arms. Be honest, be direct, and know your audience. You don't want to waste your time, and the coaches don't want to waste their time. Truthfully, it is something that you should be aware of but probably not something to be terribly concerned with at this time. Set the right expectations with everybody concerned and this has a much better chance of working out well for everyone.
In our experience, there are a number of D1 & D3 programs out there that know how to deal with the type of academically focused athlete you've described. It is going to take some work to find the baseball and academic fit, but you have a lot of time. I'd start with College Navigator to get an initial list together based on the major or majors your son has interest in. .http://nces.ed.gov/collegenavigator/. BTW - Kids change intended majors, so factor in some flexibility.
Good luck. This place is a fantastic resource.