Shin'en has updated their official website to reflect Wii U development. Here's the blurb that confirms Wii U support.
Welcome to Shin'en's web-site. If you're interested in our services and productions, you've come to the right place. Shin'en was founded in 1999. We develop high quality games for WiiU, Nintendo 3DS, Wii, Nintendo DS, Game Boy Advance and Game Boy Color using proprietary tools.
Very happy to see that they're going to provide support for the platform. I can't wait to see what they do!