I'm in the process of switching to Atom as my daily text editor (from Sublime Text 3) and needed to have my UI element font much smaller. Doing this in Atom is blissfully easy, just edit your styles.less file and you're done. The trick is understanding which elements you want to style.
Most elements I needed re-sized are easy:
The styles.less is accessible directly in your $HOME/.atom directory, or through Atom itself in Settings -> Themes.