The story about the plague and Hesiod's bones was recorded by Pausanias, a Greek geographer of the 2nd century C.E who traveled all over Greece and wrote down things that fascinated him (and holy relics and celebrity bones were among those things). It was supposed to have happened in the 5th century B.C.E, a period when "hero bones" were much-sought-after relics.
Hermes knows that those large bones didn't belong to Hesiod, but he doesn't know what they really are, since they are much older than him. Zeus and his siblings were born some time during the Minoan period (2700 - 1500 B.C.E) in my comics. So they are actually relatively young.
The natural philosophers in ancient Greece normally rejected or rationalized away popular myths, seeking natural causes instead of divine intervention to explain things. Unfortunately, no surviving writings by the philosophers mention the big bones that caused such a sensation among their countrymen (Adrienne Mayor suggests that their silence seems to reflect an eternal tension between academic science and mass culture). Theophrastus' treatise On Petrifactions described fossils and it is possible that he also mentioned hero bones, but that we will never know since this work has been lost.
Harry Turtledove (aka HN Turtletaub) touches on Classical paleontology in his series set in ancient Greece.