Nintendo will apparently continue its policy to ship its handheld gaming system with region code protection, while prevents games to function across multiple generations. So if you happen to be in Japan or in Europe on a vacation or a business trip, you won't be able to run a game purchase there on your 3DS.
It is not unusual for Nintendo, as the DSi and DSi XL consoles integrate region codes as well, while the original DS and DS Lite versions were region code free. Typically, these region codes separate global geographies such as North and South America, Japan, China, Europe and Oceania.
The high price of $300 of the 3DS suggests that especially enthusiast gamers may adopt the 3DS first and it has been especially this group that complained about region codes before as it forces them to wait for certain games and prevent the import of games from other geographies.