From an interview with Genndy Tartakovsky -
"What type of animation is Samurai Jack?
GT: The medium is the most traditional animation
you can find, except that we put it all together
in the computer. It's just a compositing tool. But
otherwise, Scott [Willis] paints as classic as you
can get, and we draw with pencils and paper, and
the animators animate it normally. So, there's no
trick. I'm a kind of animation purist. I like the
truest form of animation, with great cartoony
characters, really fun to watch animation, and
good storytelling. So, it's as old as you get."
If the animators animate it normally, then there
should be cels, yes? ^_^