I'm specifically interested in the early Spanish and Portuguese colonization before widespread immigration.
Humans can be asymptomatic carriers of diseases without being infected by the diseases. Smallpox wasn't always an extreme case with 100% mortality rates among Europeans either- it's very possible for someone to develop a more mild case of smallpox during the Atlantic crossing and survive, mostly due to antibodies built up in European immune systems over dozens of generations. Also, much like chickenpox, if someone had a mild case of smallpox as a child, they can get smallpox again as an adult.