I'm afraid I'm a bit too distant to answer all of your questions; but, here's what I do know:
First of all, if you haven't already found it, the National Club Baseball Association has a terrific resource available to you in the form of their website: http://www.clubbaseball.org/Default.aspx It not only names all of the schools that field teams, but also gives your son links to their websites.
While most of the larger universities seem to have club teams, their prowess doesn't necessarily follow that of their varsity teams. That makes for an interesting mix of larger and smaller universities at the top of the heap.
We've known several players who chose the club baseball path over the years, and they all seemed to enjoy the opportunity it gave them to continue playing without interfering too much with their academic pursuits.
Regardless of which path your son chooses, best of luck to him!