I've flitted backwards and forwards with the sibling relationship between the two (only in Ocarina of Time, mind you) for a while - all because the first (possibly second) time you talk to the ghost of Sharp the Elder he tells Link:
"I don't know why, but when I look at you I am reminded of Princess Zelda"
Plus Impa's whole, "only royal family members are taught this song" bit... made me think "Hmmm...", and we know that Shigsy likes Star Wars, at least I'm sure I read it somewhere...
I was also certain for a long time that I came across a gossip stone that said that Zelda's mother had gone missing in a war years ago, but I recently did a clean sweep of all the gossip stones and it's not there, so I must have dreamt it up. Weird.
Currently I'm of the mind that they weren't brother and sister - maybe the comment made by the Sharp ghost was just a little in-joke given the whole thing that went down with the "Link, Zelda is your..." in
ALTTP.
Actually, come to think of it, I've not spoken with that ghost in ages, I might have imagined that dialog as well... though I can't think I'd just randomly make something like that up.
This is where playing videogames too late into the night gets you.
As for the Manga - if it had anything in direct conflict with the game, then I'd tend to think that it can all be taken with a pinch of salt. If it was canon then there would be no conflict with the game at all surely?