The next time you open up the 3DS eShop, you'll be prompted to update your system hardware, to version 5.0.0-11U. While not a drastic change in the 3DS user experience, this firmware does offer a few tweaks that sound useful.
For example, you won't have to exit the eShop anymore for "Download Later" to work. Just close the 3DS and downloading begins. You can also download game updates in the background. The update also makes the save data transfer tool available, so you can move save data from a packaged version of a game to the eShop version (but not back!) The firmware also makes unnamed "further improvements to overall system stability and other minor adjustments."
Apparently, however, Japanese users have been experiencing trouble with the firmware update. We're checking with Nintendo of America to see if the same error messages are in danger of occurring here.
Update: Nintendo of America acknowledged the issue. If an error message prevents you from updating, turn the 3DS off, then turn it back on, while holding the L, R, A, and Up buttons.