What I'm asking is that I could use storage on the gamecube when I play the game. But it seems to be more difficult when play it on the Wii. On a GameCube disc. Since Super swimming is fun, Is it possible when I play the GameCube disc of Wind Waker that I can use storage and in turn, Super Swim?
Yes. Gamecube games perform exactly the same on the Wii as they do on the Gamecube. Playing games on the Wii has no impact on what glitches are possible.