Really, I wouldn't be all that surprised if there wasn't one. With Wii motion-plus the focus is going to be on the sword anyways, and since the title is "Skyward Sword", obviously there won't be a main story item that's an instrument.
Personally, I would like to have an instrument. It's always neat having different songs each with different magical effects, and that's one thing I missed in TP. I mean, I know they had the wolf howl thing, but that was just to give you new sword techniques, and the whistling grass was hardly ever used.
I wonder what kind of instrument would work well with Wii Motion Plus, because if they add one they're likely gonna want to incorporate motion controls in its use.
If you think about it, a baton, like the Wind Waker, would probably work best with Wii motion-plus. It seems like that would feel most natural to me. Perhaps you have the ability to conduct the Goddesses with your sword or something. Sounds a little weird, but hey.
Either that, or a drum set.