I'm pretty sure Miyamoto was involved with Minish Cap even though Nintendo as a whole was not.
I heard it somewhere. I don't really have a source to back me up, though.
Miyamoto has already handed several games entirely over to Aonuma. Him retiring wouldn't be any different.
As for Aonuma retiring... what makes you think someone else couldn't continue the series without screwing it up? I'll admit it would be a grim prospect, but I don't think it would...