I updated my three systems without issues. Two of them had the update downloaded and asked me to install it when I opened them, the third told me to update when I tried to enter the eShop.
From what I see, the following bits of "update data" can be downloaded from the Japanese eShop:
- Animal Crossing (1.1)
- Oshare de Kawaii! Koinu to Asobo! Machi-Hen (1.1)
- Inazuma Eleven Go 2: Chrono Stone Neppuu (1.2)
- Inazuma Eleven Go 2: Chrono Stone Raimei (1.2)
- Style Savvy (1.1)
- Fantasy Life (1.2)
- Nicola Kanshuu: Model Oshare Audition Platina (1.1)
- Professor Layton vs. Ace Attorney (1.1)
- Medarot 7: Kabuto Ver. (1.1)
- Medarot 7: Kuwagata Ver. (1.1)
- Dr Kawashima's Devilish Brain Training (1.1)
- Sengoku Musou Chronicle 2nd (1.1)
- G1 Grand Prix (1.1)
- Tantei Jinguuji Saburo: Fukushuu no Rinbu (1.1)
- Penguin no Mondai: The Wars (1.1)
- Culdcept (1.1)
- New Love Plus (1.2)
- Flora and Fauna 3D Field Guide (1.1)
- Dragon Quest Monsters: Terry's Wonderland 3D (1.1)
- Danball Senki Baku Boost (1.2)
- Metal Gear Solid 3D Snake Eater (1.1)
- Dynasty Warriors VS (1.1)
- Kingdom Hearts 3D: Dream Drop Distance (1.1)
- Mario Kart 7 (1.1)
...that's way more than I expected! The European eShop probably has less. Let's see:
- Style Savvy (1.1)
- Mario Kart 7 (1.1)
If anybody wants to check the US eShop, I found these by limiting the price range to "Free - 0".