A pretty cool topic to theorise about. I really enjoyed reading how you guys try to put things together.
I absolutely agree that the rise of the veneration towards the Triforce helped immensely to bring the creators to people's knowledge. Another reason the Triforce is important is because it ties the idea of how the world is created, by the time of the Hero of Time, the myths passed to Link completely neglect any mention of Hylia or being part of a city in the sky. I can only recall a reference to a belief of Hylian ears being elongated so they can hear the calling of the Goddesses.
Linkle and I agree that Hylia worship may still exhist in Hyrule and has either took on a different form as leadership through the Royal Family, or just lost popularity eventually fading to have very few followers left.
Maybe it is a bit of both: I think Hylia is now mostly known as one of the legends told by the Royal Family and if they are followers around, probably they don't know that Zelda is the reincarnation.
The reason for Hylia fading from fame in Hyrulean legends, might had to do with her being incarnated in Zelda. I would even suggest the same Royal Family tried to hush this fact. As it stands having people drooling greed over the TriForce was dangerous enough like to have people targeting the Princess as an attempt to destroy the cycle in hopes to weaken divine intervention. I think the Kingdom tried to switch the adoration into the three Goddesses instead and just passed among them the real origin story. Even though, probably other versions were also taught orally from the same residents they probably lose credence or were blended into the Golden Goddesses as the time went by.
Regarding the identity of the Goddesses of Time, in the Oracle of ages, Nayru controls time, which subtly suggest it might just be another name for her, while another game, I think Phantom Hourglass, instead describes Farore as the Goddess of Time and Courage. This is somethinG I wanted to say from when I started reading about the possible connection but as I kept on reading, you guys really make sense. I never thought much of Zelda being the Sage of "Time" in Ocarina of Time. Let's say the knowledge of Hylia is only another Royal Family legend passed down by generations, it would make sense Zelda used her in her prayers to keep Link safe. I don't know why I never really stopped to think about that connection.
Anyway, during SS a lot of crazy things happens and then we have wars in Hyrule, it is not crazy to think that some portals or stuff, made some of the Hylians separate into a parallel world (or outside the kingdom) and they didn't lose all of their knowledge. If Hylia was known as the Goddesses of Time and this split came before she vanished from memory in Hyrule (between before and just after SS) then it would make sense that the believe in a Goddess of Time was maintained even if her name in itself was forgotten. We know they're parallel to Hylians but they never call themselves that, which implies they don't share the Hylia knowledge or at the very least, said knowledge is fragmented and missing important details.