If I have the game card-copy of New Leaf, is there any data stored on the SD card? I ask because mine is full and there's a game I want from the eShop so I was thinking about buying another SD card. My question is, if I replace the SD card, will I still be able to play my town with any SD card in my 3DS?
Yes, it just uses the SD Card for Spotpass and Streetpass, and when you start up with a different SD Card, you'll be able to get Spotpass data on the new SD card too.
If your current SD card is kind of small and you are going to upgrade to a bigger one, your best bet would be to copy your data over to the new card. Nintendo has a walkthrough.