I know it is an old question, but it comes up in google as a first choice if you ask it.
I did ask it, as I had the same problem.
The solution is simple and I found it by chance, you need to set the “language” (or whatever it is called) of the editor to the language that you are writing in.
At the very bottom of Atom you have a strip. On the bottom right corner you have the encoding (say UtF-8) and some other things. There you have the language of the file, for example mine said “Plain Text”. Click on it and choose Julia. Now the formatting for Julia and the shrotcuts would work.