When the DS's The Legend of Zelda: Spirit Tracks showed up in bargain bins four months after release, for less than the price of lunch at McDonald's, it was rather embarrassing for Nintendo. Rumor has it the 3DS' Ocarina of Time will get a small shipment to avoid such a fate.
The comes from Sinobi blog, for whom Andriasang vouches as a good source on retail info, and it sounds plausible. Rumor has it Nintendo is not allowing retailers to place orders for the game and allotments will be small, regardless of retailer size.
The small shipment may also be due to unannounced-yet-inevitable plans for a 3DS/Ocarina bundle, as plenty of buyers are waiting on that game's June release date to go ahead and pick up the new device. Either way, for those who want to be assured of picking the game up on release day, a preorder is the way to go.
Nintendo Plans Small Shipment for Zelda 3DS — Retailer [Andriasang, thanks SecretMoblin]