And Kairu, those were guards, not necessarily knights. But the knights almost certainly exist in OoT, probably within Hyrule Castle. The shield that Link uses is a shield used by knights.
... they were wearing knight armor. Come on! You're just nitpicking there. ^^' Meh.
Yeah, TP's ending does muck with things, but I think it's still vague enough to, oddly enough, fit-just-about-any-theory.. because the G-man's ending is the most vague it's ever been. I'm forced to wonder if it didn't go like this...
Writer A: Ganondorf HAS to be in this new game! It wouldn't be right to leave him out! Zant doesn't carry the story by himself!
Writer B: but.. his history is so convoluted already, how do we put him in?
Writer A: oh blah, he escapes from a seal, gets sealed somewhere else, escapes, comes out, gets sealed.. it's fine.
Writer B: mutter mutter.. I'm just gonna have him get killed and not show it. He's come back to life as many times as he's been sealed and unsealed.