Do game cards and digital copies have separate saves?
Solution 1:
As the 3DS does not save cartidge save data to the system or SD card, there will be no clash between the two instances. They will be treated as separate games, with one file being on your download instance, and one on your cartridge.
StreetPass and SpotPass hits should go to both copies. Nintendo has fairly recently made available a tool to move save data from cartridge to download versions (albeit not the other way), so if you'd ever feel the need to do that it's completely possible.