There's finally an action replay for the 3ds? Awesome! 
I used to hack my WW game so any negative effect would depend on the code/codes you're using.
I don't know if the 3ds is the same, but if you drop building seeds too near to other buildings, you might make the game crash or lose access to other areas.
If you're gonna hack your game, I'd say do it on a spare cartridge or digital copy to experiment what you can and can't do