Anemia would not show up in the bone structure. Deficiencies of vitamin D would. Vitamin C deficiency could manifest in teeth and gum issues. Otzi (the frozen, mummified, 5300 year old, Austrian) gives us a glimpse into some of the health issues that someone even in the first millennia would experience. Calorie intake and protein availability does influence size and muscle mass. Infectious diseases being the most common cause of morbidity and mortality. Tuberculous will infect the bones, as an example. Traumatic injuries are obvious in the bones. Heavy metals used in medicine (arsenic)or from smelting/working metals will show upon bones too. Bones can really tell us a lot.