There were more in Mexico and Central America, but not so many in the US or in Canada.
Americas current largest tribe, the Navajo, barely had 7,000 tribal members in the 1860s, which was an all-time historic high for that tribe, before the reservation system began. Now there are nearly half a million of them.
The Navajo were in a vast area and were adept at hiding. There were probably a dozen slaving expeditions out at the time he was there. I think that he rounded up only about 25-35% of the Navajo. The rest took to the hills. It was enough to break the back of the Navajo as a cohesive force. There are still numerous stories on the reservation of people watching from hiding as their brethern were dragged off to the Long Walk. There were also thousands of Navajo being held as slaves up and down the Rio Grande Valley.
To this day the mention of the name Kit Carson will draw you stares of bitter hatred from the old people on the Reservation. In some cases it is the only English name they know.