When it comes to D3 there isn't much of an offer other than roster spot. Sure there is academic money that can be considered, but in terms of negotiation there is nothing that can really happen. You either qualify for the academic money or you don't. That is based on simple stats (SAT/GPA/ AP etc). Unfortunately there is no fund the coach can stick his hands to and pull more money out of for your son. The academic money is at the sole discretion of the school and if your son isn't in the top 25-50% of accepted students it is unlikely he will receive any and won't find out until after acceptance.
As for why the "offer" didn't come, it sounds like the coach took a look and doesn't believe your son will be receiving academic money. However there is still time between now and the application deadline to get ACT/SAT up and change that.
I don't think you need to be wary or cautious when it comes to other schools. I just think if you're looking the D3 route you need to understand that there are no longer offers, just roster spots. But if money is a factor, the D2 option sounds like a no brainer. And most likely better baseball. IMO