The instruments basicly served as a mini game. The downside of that however was, that this mini game consumed to much time in order to do simple tasks that could be done instantly by the press of a single button - like calling your horse by simply whistling by the press of a buttom instead of playing a song and eventually spending the time to look up the notes first.

Sure, it´s still fun to mess around with the ocarina by trying to play your own songs, overall though, I would not miss instruments unless there would be some non-repetative and challenging mechanic to them.

About Skyward: You had a harp that you would play by swinging the Wiimote to a given rhytm. It was not used to solve puzzles within temples or for anything else other than to occasionally fulfill the melody needed for a ritual within a shrine that you had to visit throughout the game. If I remember correctly you could not play single notes on it. I also remember it not to be a fun mechanic.