Yes. Early indications from GDT were that the 3-D option had not been discussed much, so speculation was that it would not be filmed in 3-D. However, as part of the ‘green light’ announcement made on October 15, 2010 it was announced that “Both Hobbit movies will be filmed in Digital 3-D, using the latest camera and stereo technology to create a high quality, comfortable viewing experience.”

Useful Links:
Hobbit green light and 3-D announcement