Some mangaka use computers, Akamatsu does (and has for years), but a large number of them still do it the pure pen and paper way.

There are a lot you can do with tablets, but a lot of the really unique things about pencils and inks can't be replicated without more effort than the regular way does.

By chapter 70, out today, they are still doing it the old way. It works. *shrug*

That said, Bakuman does a pretty good examination of different mangaka personalities and work styles. That's part of the massive charm of this series.