So I went to the eShop to get the update for Sakura Samurai and noticed a couple of titles had updates and none of them are listed in the Update section. They can be found in Settings/Other and in the 'Your Downloads' section.
There are updates for Donkey Kong, Double Dragon, Gargoyle's Quest, TwinBee, Urban Champion, Pyramids, The Ambassador Certificate and Sakura Samurai.