The Nintendo Points cards available on store shelves today will have absolutely no effect on the 3DS's virtual download store, because for whatever reason Nintendo will be making new cards specifically for the 3D handheld.
That detail was announced on Nintendo's Japanese website, which according to a translation says, "Prepaid Nintendo point cards cannot be used with the Nintendo 3DS. Prepaid point cards that can be used with the 3DS will go on sale at a later date."
Wii Points cards were first introduced in 2006 right alongside the launch of the console. When the DSi was released and digital downloads became available there, all existing Wii Points cards were valid on the DSiWare Shop. The cards were later rebranded as Nintendo Points cards but nothing was fundamentally changed.
So it looks like you'll have to buy separate points cards for the 3DS and the DSi/Wii. Hopefully that won't cause too much confusion (it will).
Feb 16, 2011