That's impossible because Zelda is attacked by Yiga footsoldiers in one of Link's memories.If I had to guess, I'd say the clan was only formed around 20-30 years before BotW.
Honestly the game is kind of inconsistent on when the Yiga was formed; Cado says they formed when the Sheikah were shunned 100 years ago after the Divine Beasts and Guardians were turned against the people, but then there's the memory I just mentioned. Makes it hard to pinpoint when they were formed.