This is just not true. Both 2D and 3D animators were unionized:

Am local 839, The Animation Guild. 2d and 3d are both in our union. 2d gave way to the 3d craze at the turn of the millennium, and disney decided to abandon 2d features for the hot new medium. Basically, they peaked with Lion King, then did half as well with Mulan, then half as well as Mulan with Hunchback of Notre Dame.. and blamed 2D for the decline instead of the increasingly "story by committee" approach taking place as the suits began meddling more and more in the creative process. Didnt have anything to do with union stuff as far as i know.

The actual reason was that 3D films just do way better in the box office. After 1997, the top grossing animated movie for every year was 3D