That won't stop third-parties from using CryEngine.
Crytek, developer of Far Cry and the Crysis series, is not currently developing for Wii U. The news comes from an interview with Golem.de, a German website. The statement, loosely translated, states that there will be games that run on Wii U using CryEngine, but they will be licensed. The interview also notes that Crytek are not developing for PlayStation Vita.
Although Far Cry Vengeance was released for Wii, it was ported by Ubisoft Montreal. Crytek has not released any titles on Nintendo consoles to date.