well, I know for a fact link has a little bag he keeps things in around his waste in TP. but in wind waker he pulls stuff out from behind his sheild. I just asumed it was a magical subspace of the game or 'canon' for every other game that didn't really explain it well
It depends. Midna holds onto his stuff in TP, (when you get the sword and shield she snaps and the sword and shield become twilight) but in other games I don't know. I think it's like a magic pocket that is bigger on the inside then it is on the outside. Like the castle in the fishbowl in Fairly Oddparents.
This is a basic concept in video game design. It has literally no explanation; it's only part of the game. Some games or fiction do make effort to explain it, sometimes where the character literally carries a magic pouch. However, this is only relevant when actually stated as such. Since it never is in Zelda, it's just part of the game.
I believe it is only a game mechanic, there is no way we can figure out where he keeps his items. Like Axle said no possible way. If you were to think very indepth I guess you could say he keeps it in a magic pouch or his companion carries it.