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? ^_^