Haven't the Sheikah always been considered Hylian?

No, they haven't - at least not according to my memory of older games or the wikis I just checked to verify!

The only time I can find where they've been cited as such is specifically from the TotK distinction, which is why it feels so weird for the game to retcon it across the board. In prior games and canon, Sheikah were considered a separate human people/tribe similar to the distinction between Hylian and Gerudo. (The term "human" used to be a separate distinction waaaay back in the day too, but then it seems to have gotten rolled into an umbrella term by around Skyward Sword.) To make matters even MORE confusing, there's always also been the term "Hyrulean" - this has historically referred to all citizens of the country of Hyrule, not just the Hylian ones. So in that regard, while Sheikah were not Hylians, Sheikah were Hyruleans. However, TotK seems to merge these two terms now as well(?)

I don't have a huge problem with changing all that wording normally! It's whatever, sometimes you mess with your worldbuilding for whatever reason. I think it's primarily an eyebrow-raise because the change comes with the additional knowledge that the Sheikah were recently subject to a canon genocide. So it's a weird choice to retcon their race into a subrace without acknowledging it in-universe. One could say "yeah, they're a subrace now, on account of the whole genocide thing" but I .... don't think Nintendo is trying to make that point, else it would have (or should have) been stated.

Thanks for your ask!

(also i'm worried about all the Sheikah/Hylian asks being posed on anon, so I apologize if I've intimidated anyone. I know the Scotland/UK ask really threw me off, so I reacted jokingly to it without ever "answering" it, but I promise I'm not weird about discussion asks unless the asks themselves are Weird)