(Caveat: I am not at all an experienced YGO player.)
Don't think of it as a single card. Think of what the card does as part of an entire deck with a clear gameplan.
A bit of research shows that the original 2004 banning was because of a combo that would strip both players' hand and field, then break symmetry by allowing you to search up Yata-Garasu. At which point you've got a hard lock they can't break out of, since you're denying them the draw every turn.
Okay, whatever, that's just one deck, right?
But, more generally, what happens when you play Yata-Garasu? It means your opponent needs an answer for it right now or they will never be able to answer it (since it'll just keep eating their draw phase). The card's tiny stats just put some conditions on the lock, but "kill your opponent's stuff" isn't exactly a big deviation from what a good deck wants to do anyway.
It's not a card that will steal the game single-handedly, but it's very, very good at closing the door on an opponent's chance for a comeback. That makes it a ban-list contender, especially as part of a dominant deck. A secondary concern that may have also influenced the decision is the "feel-bad factor:" the rational response to a hard lock is to scoop rather than play out being pecked to death, but it feels much more like surrender than losing the game normally does.