Maybe don’t update your 3DS firmware yet
There’s a new 3DS firmware update out, which you’ll be prompted to download when you load up the eShop. But there’s some kind of problem with it in Japan, prompting Nintendo to post this info page. People get error messages saying that it can’t be updated. Maybe worse?
In any case, I asked Nintendo (for Joystiq) and will let everyone know when I hear anything. And for now, just go to work/school instead of doing eShop stuff.
The update, by the way, provides a new tool for transferring save data from a retail cartridge to the downloadable version of a game, as well as improvements to the eShop (you can now download queued games while in sleep without having to close eShop first).
[Update: If you do update and have this issue, press L, R, A, and Up while the 3DS is turning on, as noted in that Nintendo of Japan document. This should force a system update screen. Thanks, supalewigi.]