First thing's first: There is a timeline with many different Links and Zeldas throughout the story.
That being said, let's get to business. I never heard any such thing of Zelda in OOT having a brother, so I'm not sure about this piece of evidence unless I missed something in the playthrough.
Aside from LTTP and supposedly OOT, what other games stated they were brother and sister?
Zelda dreaming of Link could be considered a connection between the two because both Zelda and Link are incarnations of the Goddess Hylia and her Chosen Hero. At least, that's how I've always thought about it.
The uncle saying that line is also a bit iffy because it's been shown that's not what he meant, but even then I always had the feeling he was trying to say "Zelda is your destiny" or something along those lines. Also Link in LTTP has the blood of the Knights of the Royale Family running through him, meaning he couldn't be a sibling to Zelda in that incarnation anyway.
In short, I find it doubtful that they are siblings.