There are some pretty serious performance issues with find/replace. From what I have heard, these issues are tied to Atom core rather than the find-replace plugin, and since the Atom core issue tracker is closed right now this is the best place to file an issue (though it supposedly already exists in the Atom core issue tracker)
e.g. stripping the newlines from a ~300 line file via
find: "\r|\n" and
replace: "" can take upwards of 10 seconds, and it completely locks Atom up for the duration.