It’s not great phrasing I agree… but it is a common way to describe it.
It’s the action that matters not the description.
If “she” (not clear who) moved her head back and forth in a vertical rotation, it doesn’t matter if you call it “shook her head yes” or “nodded”. The meaning is the same.
If she moved her head back and forth in a horizontal rotation and this person interpreted that as a “yes”, then that is insanity.