I can offer some assistance since I have sailed with two kiddos on the Sun.
"any great books to ready the kiddos for the adventure?" Sure, there are quite a few at the children'sbook store, I even bought one, but can't recall the name of it. It had neat little pockets and stuff inside it with invitations and different hands on things for the kids to discover and explore as you read to them about the Voyage.
"have you used the on board children's activity programs? " Yes I highly recommend the Kid's Club on the Sun. Gnat the Brat was the manager there and we sailed with her on the Sun and the Spirit, She and threst of the staff know how to have a great time with the kids
"land excursions appropriate for a Preschooler in Belize & Honduras?" I would recommend a glass bottom boat tour at Caye Caulker. That way the adults can take turns snorkelling and watching the kiddo and the kiddo can see the nurse sharks and stingrays and the beautiful coral and fish.
I've never been to Honduras, so I cannot say what I'd do. You might post this question in the Family Cruising forum and I am confident you'll get a response.
Also, how does the car seat aspect work, have it in tow for all on-land excursions? Ours is skinny and still in cumbersome 5 pt. harness type seat. i wonder do the ships ever have car seat rental since stowing it in cabin seems like a drag?
I always bring backless boosters for the kids on vacations. They are under $20 at Walmart and I buy an XL ziploc bag and stick on a lugage tag and check them with our lugage at the airport. but then use them in the cabs to and from the port/hotel etc...