Suppose the creators had named the boy "Big Creek" instead of "Little Creek." This is perfectly plausible, since the adjective refers to the size of the creek, not the size of the boy. What would this name tell us?
To me it would cause some cognitive dissonance. Big Creek sounds like a strong, tough, independent character. I expect him to take on anyone, up to and including an Army colonel, without assistance.
In my mind, Big Creek is an accomplished warrior. He doesn't need a horse to make him complete. Little Creek does.
The boy has a "little" moniker for the same reason Little Tree does. For the same reason so many Indian women have names like Little Flower or Little Moon. The diminutive name diminishes them.
The lack of adult Natives leads to the same result. It diminishes the richness and complexity of Indian life. It conveys the idea that Indians were scarce in the area—i.e., in the process of vanishing. That white men were the norm and Indians were the exception. In reality, it was the other way around.