As far as we know, yes. We don't know much of the details except that you have an ID and a password. Whether the ID is alphanumeric or just numeric, and whether Nintendo will allow multiple systems to use the same account (useful for all those "but my Wii dun broke!" doomsday scenarios the Ninhater brigade likes to tell themselves at night to make them feel better about shitting on Nintendo's digital efforts) remains to be seen.
And yes, these points can be used for anything on the eShop (Virtual Console, original software, full game downloads), and that apparently extends to 3DS as well. Probably the whole point of the Nintendo ID, actually: linking your Wii U and 3DS.