The biggest drawback to the "Haki has always been there" theory are the instances where it didn't happen.
Zeff was supposedly dropping hints about it but actual one-time New World pirates Crocodile and Moria didn't use it?
Why did CP9 train from childhood to use inferior versions of it?
Why was Blackbeard hurting Ace with the Darkness Fruit meant to be such a big deal, when it turns out it was actually pretty easy to hurt him?
And why did Blackbeard gamble his entire Pirate King dream on finding the Darkness Fruit when it's most notable feature is so easily replicated?
I think it's much more likely that Oda realised he needed another power set alongside Devil Fruits, and going back through his work, pulled together various unrelated (At the time) powers and feats and turned them into Haki as we know it today.
Oda definitely has a lot of the story at least roughly planned out, but some stuff was very much a later addition to problems that cropped up as the storyline stretched out with (IMO) Haki, Sabo and the Niku Fruit being the most obvious examples.