Or OPverse was different then, Oda didn't plan for everyone to have coa, coo. So in a way, BB-Ace was one of the last haki-less fights in OP.
So? Doesn't matter. We update. That's all there is to it. Unless it contradicts something very important that threatens (or already did) to completely break the verse's laws, you should just accept past feats in light of new info. Which is not that hard to do in Ace's case given his background, potential, encounter, reputation etc. Besides Luffy (by virtue of being the main character), no one holds a candle to Ace among the young generation.
Also by the time that Banaro fight happened, CoO and CoC already showed up. And Oda likely thought about how to deal with Logia when he created them. Relying on finding out individual weakness every damn time is not that easy, especially for a main character like Luffy who is not brainy (Figuring out Croc's and being immune to Enel's by pure luck is the limit. Anything more is too contrived). Ace was even 100% relaxed when BB said he was a logia which means Ace had a way to deal with Logia intangibility. Right after that he noted that ''an attack like this (the firefly one) should not hurt you (BB) if you were a Logia''. Which kinda means there are indeed other kinds of attack that can work.