I sincerly doubt they're using transparencies... everything is done digitally now. It's much cheaper that way.
Traditional animation is done by first drawing out keyframes which capture the important poses and framing. These are done by the lead animators traditionally (when you see animation story boards, they are usually rough versions of these). The keyframes are then given out to the animators who then actually draw the inbetween frames (inbetweening or tweeing). This is just a high level summary of course, there's lot of other steps and different animation passes that are done. But yes, all traditional animation whether it's done on an animation board or purely digitally, is hand drawn.
It isn't really reminiscent of 3D art at all, unless it's being done in flash or something along those lines (which caries with it a rather distinctive look, see the esruance commercials or South Park for something like that).
Edit: And to add, the tried and true method if it's being done on paper is just to flip back and forth. Animation tables have lights under the table to illuminate the paper from underneath so you can see the previous frame or two as you're drawing the next one. When everything was done on paper back in the day, the frames would initially be drawn like this and transferred to transparencies later, IIRC.