It is just somewhere to transfer your Pokemon to. It doesn't seem to affect them outside of the fact that they are gone from the DS game. If you transfer up to 250, you get Phione, and if you hit 1,000, you get Mew (I have yet to do that, actually..)
It's Nintendo's way of giving out rare Pokemon to people who don't live in New York, or have access to someone who lives in New York (er.. that is where the Nintendo Store is, isn't it?)