Nintendo has apparently fixed the issues plaguing the Nintendo eShop for the Wii U and 3DS and things should be running normally, more or less. Users may still have problems redeeming download codes but Nintendo has a temporary solution (visit "Your Downloads") for that.
Unfortunately it looks like the Pokémon Bank and Poké Transporter releases are still delayed for the time being as the company sorts out those issues.
Take a look at their latest update from the Nintendo Facebook page.
The Nintendo eShop is now available on all systems. We do not anticipate any further outages, but will continue to closely monitor the situation. We sincerely apologize for this week's inconsistencies and thank you again for your patience and support. We will share more information about the launch of Pokémon Bank and Poké Transporter as soon as possible.