i agree with you and your P.O.V on the sheika that are left,Shiekah don't go missing until after Ocarina of Time. We know this for a fact because they were a figure, like a secret service to the Royal family that was nearly wiped out towards beginning of Ocarina of Time. After Ocarina of Time's Impa died they weren't mention predominantly again until Breath of the Wild, and Breath of the Wild is a rabbit hole of inconsistencies.
but i thought this was a clear reasoning?
"We are implying that the "Dark Sheika/Interlopers" were banished in great numbers, during the Era of chaos.
So point being, After the war in the "Era of Chaos", there were limited amount of "Sheika" left.
We're not implying they were All banished into twillight, that goes against the lore.
A large majority were "imprisoned" and the few remaining "Sheika" were kept close to the Royal family.
#Side note,
If the Triangles in the "Sheika Eyes" Lashes, symbolically refer to the "Triforce" (The Godesses Sacred Relic)
Wouldnt the "Interlopers" Denounce The Godessses and also the connection to the Triforce?
Removal of the triangles in the "Twillis/Sheika Interlopers eye suggests this as a plausibility.
Unless there is another race we dont know about that uses a "Eye" symbol like the "Sheika" do."