The Scenario
Greater Sci-Fi combatant
I feel it should be noted that the Sky Cannon is designed for use by the Ooca. That is, a species of birds who are between roughly 1 and 2 feet tall and can fly/hover. (I would also swear they are ancestors to the Chozo but that is beside the point.)
You've heard the phrase, "the bigger they are, the harder they fall," right? It also works in reverse: the smaller they are, the softer they fall. An elephant could break its legs from a fall of a few feet, while a cat can be expected to survive a two story drop. In any case, the smaller something is, the lower its terminal velocity is. That is, the maximum speed something can achieve from gravity alone, and/or the distance it needs to fall to reach this speed. What I'm getting at here is that the Ooca are small enough to have a low terminal velocity, and can also slow themselves via feathers and/or flight. They can be reasonably expected to survive both trips in the Sky Cannon, mostly because it's designed for their use.
You know what the Sky Cannon isn't designed to fire? A human. Or Hylian, as the case may be. It isn't a ride, it isn't designed for him, and it involves an enormous fall. Fact is, Link surviving this is an impressive feat.