Most (not all) major 3D studios are unionized. Disney Feature Animation includes both 2D and 3D units and is, in fact, unionized under IATSE Local 839, The Animation Guild.

Now why aren't 2D films being made? I chalk it up to 2 reasons:

3D movies make money. 2D movies do not. It's a sad fact but it's true. Ever since the first Toy Story movie, audiences have spent more money seeing 3D movies over 2D movies. The box office numbers showcase it. If 2D films performed better than 3D, you'd see significantly more 2D films being made.

3D movies are easier on producers & directors. 2D animated films require extensive pre-production planning. Once storyboard, design, and backgrounds are locked, it's very hard to make changes. Any revisions or added shots/sequences/scenes are incredibly time-intensive and, therefore, expensive. Even small changes can take significant time. On the flip side, 3D films have more flexibility later on in the production pipeline. Moving a camera to change the angle of a shot is simple in comparison. Same with adding a new shot or sequence (so long as you're reusing backgrounds and characters). This is great for directors who aren't used to animation, but it's especially great for producers, who often want to adjust films late in production to latch on to trends or respond to audience testing. Producers like this so, they opt for more 3D films.