If it's really true (which in my opinion would be absolutely incredible!), then I'd guess the display in the WiiU controller supports passive 3D, like for example my PC monitor does. The additional manufacturing costs wouldn't be that high.
On the other hand, since it contains an infrared LED anyway, the WiiU controller should be perfectly capable of controlling standard shutter glasses as well. It would work, without any additional cost - the 3D experience just wouldn't be very enjoyable because of flicker if the builtin screen isn't capable of high frame rates, as JoeTheBro already pointed out. But it would work, even with "only" 120Hz. Wikipedia for example mentions 100Hz as practical minimum value for active shutter technology.







