score:7
I don't have any expertise in this field, and the question doesn't provide much detail about what sources Harari may be citing. I did a quick search on Google Books but find no reference to malnutrition in Sapiens. However, just glancing at a few sources we can see that bioarcheologists look at a wide range of evidence to reconstruct pre-historic diets and nutritional status, including:
One of the most powerful and widely-used tools across all forms of evidence is isotope analysis. Measuring different isotopes of carbon, nitrogen and sometimes other elements allows researchers to trace all kinds of connections between different organisms and what they are consuming through their fossilized remains.
I'm guessing Harare may be looking primarily at the Fertile Crescent, but a lot of what comes up for me with a quick search is focused on Europe. The article "Neolithic transition in Europe: The challenge for bioarchaeology is fairly broad and not focused specifically on nutrition, but relevant as an overview. "From Health to Civilization Stress? In Search for Traces of a Health Transition During the Early Neolithic in Europe" relies primarily on human skeletons to find evidence of malnutrition among other things. "Health Status of the Neolithic Population of Alepotrypa Cave, Greece" is especially relevant and also focuses on evidence from human skeletons. The abstract gives some technical detail on evidence of malnutrition: "anemic conditions (cribra orbitalia and porotic hyperostosis), mild or healed in manifestation, most probably of nutritional origin, resulting from a poor diet focused on terrestrial resources such as domesticated cereals".