The unique ID is similar to CD-Keys for PC games. If you start sharing your CD Key with random strangers, sooner or later someone will start cheating with it. (even though cheating isn't quite possible yet on the 3DS, but that might change in the future). If that person gets caught, that key gets banned, which means you get banned to because you have the same key. So just use caution when deciding to share it. If at a later date, you find that you got banned...you only have yourself to blame.
That's it in a nutshell. Treat it like a game CD-Key or something akin to that.