I know this thread is pretty much dead, but I want to point out that me and my sister look nothing alike, and we're related. So that puts a huge hole and just theory.
If you've ever read the Nintendo Power magazine in Germany, you know that there's some Nintendo Power comics where Link is born shortly before the Civil War that happens right before Ocarina of Time, and that his father is the Captain of the Royal Guard of the comic, in the comic it is obvious...