As long as it's a cartridge, not a digital download, I don't see why it would mess up. The game saves town data to the game cartridge, so it seems that it would be impossible for the second cartridge to magically get its data deleted.
Although, some streetpass features for the game may get messed up.
"Turn the other cheek." --Punchy, AC:WW
+0 ACC Time
Yes I'd have to say you're safe getting a 2nd one. I somehow got two Wild World games and it ended up working fine but I agree that streetpass might be funky. I'm curious as to how that would work out.