According to this site, http://www.phuck-ign.com/, Nintendo is getting so sick of stores offering the Zelda bonus disc on its own, rather than as an incentive to purchase Zelda: The Wind Waker, that they refuse to make more copies of it. Now I've seen game stores bend the rules regarding release dates and promotional offers, but I've never seen them get reprimanded so severely for it. The worst part of this is that it's the customer who will ultimately suffer the most from Nintendo's actions.
Get 'yer Zelda bonus discs while you can, folks, because they may just be the next Panzer Dragoon Saga.
JR