Hi Steve. Our son took his first cruise at age 11 months -- in some ways it was easier than taking him today! (He's now 13 years old.)
I don't know the answer to your first question, other than that you will be charged for port fees. Yet, your son will most definitely be allowed in the formal restaurant. We practiced longer dinners in our dining room at home for several months before we went on his first cruise, and gradually introduced him to restaurants. He did well in the dining room. One tip is to ask the waiter to time his meal with your own. For instance, while you are having your appetizer, perhaps your son could have some crackers, or carrots/celery. Then, they could bring out his "entree" (whatever that might be) around the same time you're having yours. Makes for a less impatient child.
As far as the specialty restaurants, some have minimum age requirements. You might want to check with the maitre d' when you board, but I know he will be too young for Le Bistro...not sure about the "non-pay" specialty restaurants.