Before you start speculating as to how your DS Lite will be used in conjunction with the game, allow us to disappoint you. The DS Lite here, found in the kitchen on the first floor of Flipside, is just a recipe database that is upgraded every time you collect one of the 96 recipe cards found in the game. Wii Fanboy reader jeffoverweg also reminds us that Nintendo has been self-referential with its portable devices before: the Game Boy Horror in Luigi's Mansion, the use of the DS phat and GBA in Paper Mario: Thousand Year Door, etc.
If Nintendo were to add DS functionality with Super Paper Mario, there is no way they would have kept it a secret, especially not if it meant they could sell a few more DS units on connectivity alone. For those looking to link up their Nintendo hardware, you'll just have to wait for Pokemon.