Good news the first one I bought was a black QW4021 on Version 9.4-U so Immediately returned it while in the store and got a red unit QW1023 on 9.0-U
the setup menu is less than a minute to get past by the way.
All electronics will be charged to 50%. Don't be fooled even if it says its at 100% let it charge for a maximum of 8 hours. We aren't using nickle in batteries anymore but its still not good for a lithium battery to be pretty much at any other charge than 50% unless you run it down every couple of days.
Batteries are always charged from the factory, because li-ion/li-poly batteries don't like being completely discharged as it can shorten the battery life.
Sometimes when batteries sit around for a while without being charged before the device is sold, they can become discharged (potentially hurting the battery life), but they would have to sit around for a long time for that, and the n3DS is still new, so it's safe to say all n3DS batteries will have a decent amount of charge on them out of the box.