A bunch of people have had issues with Atom's fuzzy finder being slow:
https://github.com/atom/fuzzy-finder/issues/88
When the Atom window loses focus and is focused again it reindexes the
whole project... not a great idea on a codebase as large as ours.
It turns out that there is an alternative fuzzy finder that you can
use... it is still a bit slow when the project is first opened but Atom
doesn't take a vacation every time the window loses focus.
It is easiest to install it using apm:
apm disable fuzzy-finder
apm install
https://github.com/antelle/fuzzy-finder-with-faster-loading
Hope that helps!