There's no official text source, but a lot of places are reporting that Nintendo President Satoru Iwata announced Wednesday that they are "looking into having automatic system updates via the internet," in regards to the 3DS. This is done by a feature called "SpotPass," which will allow the 3DS to update even in sleep mode, as long as it has internet access.
No news further than that. The big question is whether you'll be able to turn automatic updates off or if they are forced. Fans of homebrew or less legal things ought to be worried if they are interested in online services. And if Nintendo handles 3DS firmware like Sony handles PS3 firmware (by completely removing features), everybody should be worried.