I think the best explanation is that when Kukui was establishing the Pokémon League, he didn't know that Hapu had become the new kahuna. Consider this: after you clear Sophocles' trial, Kukui tells you he's going to Mount Lanakila to finish the Pokémon League, and you don't see him again until you get there yourself to challenge it. Perhaps he selected Kahili to be the last Elite Four member before Hapu was chosen as the new kahuna, thus, he wouldn't have had a reason to choose Hapu at the time. If Kahili was chosen after Hapu became kahuna, he most likely didn't hear about it because he was busy trying to finish the League.