holy fuck, theyre still finding stuff in OoT? i was (passively) involved in that whole "scene" for a while and when they found the fully functioning(!!) arwing enemy i thought that was it for sure.
tho i wasnt talking about ura zelda but the original zelda 64 that was planned as a 64dd exclusive (and eventually reworked into OoT).
also truthtfully i don't think there is any actual ura zelda content in OoT's files. what they found was most likely just the "hooks" to make it work later on.
Take into account that 64DD emulation is recent - as in, I saw the news like a week ago or so? (Mario Artist runs mostly fine, except for Polygon Studio being unable to pick stuff with the HLE engine, same issue that Pokémon Snap has in fact) Now that the 64DD is emulated it'll give room to finding a lot more of stuff.
As for Ura Zelda, yeah, I imagine only the hooks are there. If there's any Ura Zelda stuff to be found, it'd be present in Majora's Mask (since that's what started as Ura Zelda originally, right?).
EDIT: er, rereading your post. If I recall correctly, OoT was always a cartridge game, and then it had disk hooks in order to make it load Majora's Mask from the 64DD. I could be wrong though, but given they did exactly that with F-Zero X, I wouldn't be surprised.