There is a pretty distinct different between the current Simpsons animation and the animation of old. It seems rather obvious that it's being done with computers rather than being completely drawn out by hand.
However, I never considered the transparency thing. I've always been impressed with hand-drawn animation. I would imagine it is very tedious work.
To me, it would be like typing the same form letter thousands of times, over and over again in exactly the same way, and every so many pages, changing a word here or there. It sounds very tedious and monotonous, but if it's something you love, I guess you just make it work.