When i re-downloaded Super Mario 3D Land on my emunand from the e-shop it reappeared on my sys nand as well.
Not sure if all icons appear but like i said i believe formatting the 3DS with the SD card inserted will unlick the two.
Not 100% sure but i believe you can remove the SD Card from the 3DS and format the system nand to separate it from the emunand.
You could also try re-arranging the icons while in system nand. I had the problem of games moving out of folder in emunand which stopped when i put them in identical...