Yeah that one was bonus to the Mario Kart Double Dash bundle if I remember correctly. I got it from Club Nintendo in any case.
Besides that one, I know there was a GameCube/Wind Waker bundle at least here in Europe, because my cousin got that one. It also included Ocarina of Time & Master Quest as bonus. Lastly, The Minish Cap was shortly bundled with the GBA SP and I think either Phantom Hourglass or Spirit Tracks was shortly bundled with the DS but I'm not sure. spurge is correct in the N64/Ocarina of Time bundle though, that existed too.
All in all I'd say it's plausible, but I hope it won't be a Special Edition because I don't want to miss out again .
Europe indeed got a Wind Waker bundle:
North America got a free Zelda Collection disc with a GameCube for $99.99 in November of 2003: