Because the empire is relatively new in the history of Tamriel. Saying it like that, then there was no lore that the Numidium ever existed before Daggerfall. Just because it hasn't shown up in lore before now doesn't mean it never happened. This is how lore is built, things previously not known or stated become revealed as the story moves along.
"The Dragon Nafaalilargus, a loyal soldier of Tiber Septim"
"It was rumored that they moved closer to Cyrodiil, and it may be for this reason that dragons are sacred to the Empire. The legends tell of their aid during wars in exchange for shelter"
Okay but this is the Septim blood line we are talking about, and the back bone to the Empire. Don't you think it would be known that he fought dragons before. It even says that dragons were loyal soldiers to the Empire, and fought in wars. So to tell me that the same person that had dragons as loyal soldiers also killed them doesn't make sense to me. Dragons were sacred beasts. Unless all the dragon fighting happened in the 200 years inbetween games i don't get it.
The dragons were defeated by cliffracers.
Yes true, but why would they attack humans when the Empire gave them shelter from the cliffracers.