Good point.
I think that the mass flooding killed 30-40%, and then another good number died during the war that followed. This assumes that the Void Century STARTED with the mass flood.
IMO, the World Government caused the Ancient Flood with the Ancient Machines, and then blamed it on the Ancient Kingdom.
After, the entire world went to war with the Ancient Kingdom, only to realize that they were the good guys when the war ended, and that the World Government were the ones who had caused the flood and war.
So, the flood started at the beginning of the Void Century, led to the war, and the Void Century (a war that destroyed history) finally ended with the war's end.
This would explain a lot, because if that led to 100 years of war, I can understand why the Gorosei and WG really want to avoid that from happening again.