On all the visits (official and unofficial) my son attended, my wife and I were included in most everything. The tours were presented to all of us (speak to son directly when it was specific to him, and address us parents when it was pertinent to us).
We were welcome to attend practices, scrimmages, games, and when invited over a football weekend (or any sport), NCAA allows the school to provide up to three tickets to you.
Prep your son for a wide variety of questions and also prep him to have some questions of his own (as BOF mentioned). You also need to think ahead of what key information you must have and ask if it isn't presented along the way.
I know your is unofficial, but on official visits, they may send the player off with other players during the evening to hang out in dorms/houses and see student life outside of school and baseball.
The school is trying to sell itself to your son as much as your son is trying to sell himself. You'll typically find the visits to be very enjoyable and informational. I'd be very surprised if you found the staff to intentionally exclude you from anything. They know that this is your 16/17 yr old kid and that Mom and Dad have as much (more) say in any final decisions than the kid.
Tell your son to be himself, be comfortable, and enjoy the ride.