I don't understand what's going on, here's the file of what I'm trying to export. If I select just one empty and try to export it, it does without issues, if I try to export several then it just stops responding after setting the name for the FBX and clicking export although it doesn't crash, it just stays there "thinking". I'm using Blender v2.78c (latest one) in Windows 10.
Seeing the same result you are, taking a very long time to process
My blind guess is that if you wait long enough it will eventually export the file successfully, since selecting only a subset of the empties exported successfully after a while, although it may take longer than you are willing to wait.
The resulting (partial) file did however have 200+ Mb in size, so something else other than geometry is being processed and exported that is causing the long delays and large file size.
I noticed that some objects did have some animations in them, so that must be causing the delay and file bloat. Disabling animation export in the FBX dialog resulted in a 500kb file that exported in seconds.
This may be an actual bug or a result of the high number of empties, heavy use of parent relationships, baking of animations, or any combination of both.