Spoilers up to but not including the flashback arc in 3rei:
In the Prisma Illya anime, the fact that Miyu's brother is (Miyuverse) Shirou becomes obvious fairly early on. The scene early on in the first season ("1in"?) where Miyu mentions that Illyaverse Shirou reminds her of her brother already points strongly in that direction, as do the short still-frames of him we see in Miyu's memories during 2wei Herz.
Early in 3rei, Illya and Gil meet Miyu's brother, and though we don't get a clear visual on him, we hear Sugiyama Noriaki speak - that settles it for anyone who had any doubt.
However, I have heard that manga-readers weren't 100% sure about the identity of Miyu's brother until he shows up to fight the Ainsworths and utters "Trace On". I can see how this could be the case - if his appearance was better-concealed in the manga, that plus the fact that the manga is not voiced could have kept readers guessing for a while.
So - what evidence did manga-readers have about the identity of Miyu's brother prior to the definitive reveal?