The "100 years ago when Ganon destroyed Hyrule" is referring to the original Zelda game where you had to collect the 8 pieces of the Triforce to defeat Ganon and rescue Zelda. Zelda II takes place about 6 or 7 years later later and you prevent the return of Ganon. However, Zelda II has towns where Zelda I doesn't. So what happened to those towns since the events of Zelda II? Ganon was defeated in Zelda I and those towns were not even seen in the first game. So something must have happened between Zelda II and BoTW where Ganon returns and destroys the towns and Link is apparently killed but put in the Shrine of Resurrection for a century, setting up the events for BoTW.