I have a N3DS setup through menuhax + AuReiNand with 10.7 emunand. Twice when I've tried to shutdown the console (using power button and then clicking at the Power Down on the screen) the console didn't turned off properly, staying on, with disabled screens, but using wifi and CPU when I folded the console. When I've arrived at home to charge it, red light blinking.
I dunno if the console actually failed to shutdown properly, or if I've got a really bad timing and made it enter at sleep mode while shutting down, but there it is, sometimes you may think that the console was turned off but it isn't. Now I actually wait for all the leds to turn off with the console unfolded.
EDIT: In case you need to store your console or other Li-Ion battery, first you should charge/discharge the battery to something around 60~70% of it's capacity, then remove the battery, and once at every 6 months, guarantee that the battery is with this charge (probably you'll have to recharge a bit). The battery shouldn't be at it's maximum charge neither next to zero.