I think your numbers are highly exaggerated. You have to be careful; revisionist history is exceedingly easy to find. You should be suspicious if the history is blatantly one-sided (as what you refer to seems to be), or if the numbers are unrealistic.
The natives of this continent were constantly fighting for limited food and resources. They were beset by diseases. The only way this continent could have supported hundreds of millions would have been if they had developed a strong model of cooperation, and more adherence to peaceful coexistance. There are hundreds of millions of people on this continent now, but only because we live peacefully, and have advanced medicine and technology. Had the natives developed a civilization model that could have supported a large population, the Europeans never would have been able to settle here. Had that been the case, the American continents would be more like India or China, with the various trade, business, tourism, etc. exchanges that we have with those countries.
The entire population of the world in the 1500s was estimated to be less than 500 million. That fact alone should make you question those sources that claim that hundreds of millions of natives were slaughtered by the Europeans.
The missing piece is that the Spaniards didn’t slaughter 90% of the people in the New World.
Diseases brought by them wiped out ten times the number killed in battle, and unlike the Spaniards, these diseases didn’t just target the leaders and native warriors, they killed totally indiscriminately.
A society just doesn’t cohere when 1/2 to 2/3 of the people die of illness, farms don’t get cultivated, crops aren’t harvested, harvests are paltry, and don’t get distributed to population centers.