Nintendo revealed that players will have the option of combining funds from the Nintendo 3DS and Wii U eShops, and will be able to purchase content from either device using shared funding. The new functionality requires a Nintendo Network ID, which is not currently required for eShop purchases on the the Nintendo 3DS.
Nintendo additionally notes that players will need to create or link a Nintendo Network ID with the Nintendo 3DS in order to download free software and demos from the portable's eShop following the release of the next system update. Paid software will not require a Nintendo Network ID.
[Update: Nintendo of America announced that next month's system update will also add Miiverse support for the Nintendo 3DS.]
[Update 2: Nintendo has detailed the Nintendo Network ID account migration process, warning that only one NNID may be associated with a Nintendo 3DS system. In addition, a single account cannot be duplicated across multiple 3DS systems. If a new NNID is associated with a Nintendo 3DS system, players will be unable to combine balances with an existing Wii U eShop account.]