Adding "well" is an intensifier -- "very possibly (it was so.)"
So the sentence could have been written
they might have been less afflicted
It is quite possible that they were less afflicted
Very possibly they were less afflicted
It's entirely possible that they were less afflicted
It's likely that they were less afflicted
The idea is that since diseases are spread from person-to-person, a small and scattered population would never be infected with a particular disease in sufficient numbers to constitute a reservoir.
So isolated bands of humans would not catch any particular disease because there were not enough humans to keep up the chain of contagion from person to person. Any disease that affected one small band would burn itself out before it got a chance to spread to others.
This changed as soon as people began to live in large groups. Then there was always someone with cholera or smallpox somewhere in the population. They harbored the germs, so anyone without immunity would end up being exposed to these microorganisms.
It was only the inventions of modern medicine that stopped this endless transmission -- vaccinations, antibiotics, and public health measures regarding clean food and water now break the chain of transmission.
But thinking about all the history before modern medicine, our first hunter-gatherer ancestors very possibly had very little disease.
That is, they may well have been less afflicted with disease than anyone else in history.
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