While some of this question is up to the subjective opinion of the individual reader, the sequence that contains the brief exchange between Kit and Nat about slavery can be found in chapter 2.
In an earlier part of chapter 2, Kit and John are speaking with each other about Kit's family in Barbados. Kit admits that she didn't have much family in the way of blood relatives, but she had slaves that helped to raise her. This shows readers that Kit has grown up with slavery. She doesn't think it is odd to have slaves.
As the chapter continues, Kit will become frustrated by the ship's slow progress and its confining spaces. She will briefly vent to Nat about the "filthy ship." Nat is very much offended. He loves the ship, and he loves the work that the ship does. Kit doesn't like the smell of the hold with all of the animals, and Nat gives a retort about Kit preferring the smell of dead, rotting human bodies in the hold.
Kit is appalled at the idea, and Nat considers that maybe she doesn't know about slavery. Kit responds by admitting that she had hundreds of slaves in Barbados, but it is clear that she never gave it a thought as to how those slaves got there. Nat defends his family's choice to never transport slaves. He believes that it is a disgusting practice, and Nat passes partial judgement on Kit for perpetuating slavery due to the fact that she had slaves and doesn't really see it as a problem.