Bricking? No. But I am curious about the error screen known as the "Black Screen of Death." Nobody knows exactly what causes it, and although I haven't used any flash carts on my 3DS, I've recieved the error a few times. Nintendo is very aware of the error, and it is easily fixed when you shut down and reboot the 3DS.
So if anything, I could see Nintendo forcing the 3DS to error when a flash cart is detected. It won't brick, but it won't allow you to play until you reboot without the flash cart inserted. Just a thought.