After updating to the latest version (0.127.0) on Mac OS X, I can no longer see the vertical scroll bar (ever), and I can only see the horizontal scroll bar when I’ve scrolled all the way to the bottom of the file I’m looking at.
Actually, I found that the vertical scroll bar is hidden only when lines in the file I’m looking at extend beyond the wrap guide. If I edit the file so that no lines extend beyond the preferred line length, the vertical scroll bar immediately appears.
I’ve confirmed the vertical scroll bar behavior on OS X v10.9.4 with Atom version 0.128.0-f872583. Can you file an Issue on the Atom Core project and link it back here?