The stories goes like this.
During a QnA on what characters users wanted for Hyrule Warriors, one asked about Vaati.
They said "That would be diffcult."
The other comes from Jason Micheal Paul, where he had directly stated that he was uanble to do Capcom Zelda Music. It's speculated it was for legal reasons, as a lot of more obscure titles, Including Spirit Tracks, and the other GB game, Link's awakening, got redone tracks.
Interesting. I managed to find them both, but I'm not sure that either one is definite proof that Capcom owns them.
https://youtu.be/96Vf08ImYJk?t=34m16s
34:16 is where they answer the question about Vaati in Hyrule Warriors, and they do say he would be difficult, but that might not necessarily be a legal thing. They could simply not know what to do with him, or perhaps the team just isn't interested in his character.
As for the Orchestra, I found the place where Jason talks about it, but idk, he sounds kind of unsure about it to me, just saying he
believes that it's owned by Capcom, which isn't really saying for sure either way.
Nikolas: What about Minish Cap?
Jason: I don’t think it is. Because Minish Cap, I believe, is a third-party game. So there’s the issue of licensing that and Nintendo hasn’t included it. I like Minish Cap, though. It’s kind of similar to Hyrule Warriors in the sense that it was a joint venture.
It's worth noting that the Oracle games were also developed by Capcom, and those aren't excluded from the Orchestra.
The other aspect of the program is more modular, so you can expect to hear highlights from other favorite moments in the Zelda pantheon that may not be covered by the 4-movement symphony, not to mention a lot of the great music found in the peripheral titles, like Majora's Mask, or the handhelds like Spirit Tracks, Link’s Awakening or the Oracle duology.
I'm not sure either of these things can be used to say definitely that it's owned by Capcom since the game itself explicitly says it's Nintendo's. It's very frustrating that we can't know for sure.