The OP is talking about an NAIA school, where the expectations are probably the opposite of the SEC. Also, in this sort of recruiting (D3/NAIA senior year), it's entirely possible that few, if any, questions have been answered before the visit. There may not have been many phone calls or texts. Hopefully the coach will answer many of them before you ask, but should know what you want answered.
I completely agree, let your son lead, his questions matter most (and may surprise you). But don't be scared off from asking your own, too - whether about housing, travel, academic support, or even trainers and facilities.
Information about a JV team is not all that easy to find on the web, although you can google "[schoolname] baseball jv" and it might come up. I would be interested to know how coaches with large (45+) rosters address this at visits - surely it's something that any recruit would want to know. But it's a very delicate thing to actually ask about.