Native Americans weren't "one thing" -- the population of North America was diverse, with different languages and cultures. To say "what were native Americans like?" is thus a bit like saying "what are Europeans like?"

Cultures varied considerably from place to place, tribe to tribe and over time. We have far more information about Native American cultures after contact with Europeans than before, and the most dramatic health concern we see is smallpox, which devastated indigenous populations, and produced all kinds of responses. Many villages were abandoned, survivors often fled; but that disease didn't exist before contact with Europeans-- and so when we talk about smallpox, that's novel.

Eye complaints including blindness seem to have been common with a significant burden of glaucoma and in places there were very also high rates of trachoma-- an infectious disease.

Lewis & Clark noted these diseases among the native Americans they encountered:

The large number of eye ailments among the Indians again impressed the leaders. Clark wrote on April 8, when the party was between the Sandy River and The Dalles, concerning an Indian woman who was blind in one eye, and of a man nearly blind in both eyes. He stated that blindness appeared to be more common among the natives of the Columbia than among any other people he had ever observed, and that they almost invariably had sore eyes at all ages, with the loss of one eye very common, and complete blindness almost invariable in old age. Clark, like others who commented on this affliction among the Columbia River Indians, was inclined to ascribe it to the reflection of the sun on the water to which the Indians were constantly exposed while fishing and to the fine sands carried by the wind. It is now known that trachoma was very prevalent among many Indian tribes.

They also describe treating many different natives for other ailments-- some quite serious, obvious, and debilitating. The fact that these folks were there for the expedition to meet is evidence that they'd not been ostracized or killed, and no "special status" is mentioned.

Lewis notes in his journal entry of 11 May 1806

[M]any of the natives apply to us for medical aid which we gave them cheerfully so far as our skill and store of medicine would enable us.    schrofela, ulsers, rheumatism, soar eyes, and the loss of the uce of their limbs are the most common cases among them.    the latter case is not very common but we have seen thee instances of it among the Chopunnish.    it is a very extraordinary complaint.    a Cheif of considerable note at this place has been afflicted with it for three years, he is incapable of moving a single limb but lies like a corps in whatever position he is placed, yet he eats heartily, digests his food perfectly, injoys his understanding, his pulse are good, and has retained his flesh almost perfectly, in short were it not that he appears a little pale from having lain so long in the shade he might well be taken for a man in good health. I suspect that their confinement to a diet of roots may give rise to all those disorders except the rheumatism & soar eyes, and to the latter of these, the state of debility incident to a vegetable diet may measureable contribute.

The only social ostracism they record is a special status for menstruating women that is familiar from many other cultures:

Lewis commented on the practice of segregation of menstruating women from the remainder of the family. The daughter of this Indian, having arrived at the age of puberty, was obliged to sleep at a distance from her father's camp and when traveling to follow at some distance behind. At other camps of this Chopunnish tribe he observed a small lodge with one fire which served as a retreat for the women during menstruation. The men were permitted to approach no nearer than fifty to sixty paces from this lodge, and if they desired to convey anything to the occupants they would throw it toward the hut as far as they could and retire.

But to say something about one particular tribe is . . . to say something about one particular tribe. Today there are some 560 recognized tribes, speaking on the order of 300 languages but historically there would have been more. Its reasonable to expect that if you looked hard, you could find a wide variety of practices.

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Sources:

Medical Aspects of the Lewis and Clark Expedition

Journals of Lewis and Clark

Smallpox and American Indians Revisited

Identity and Healing in Three Navajo Religious Traditions

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