If you use Apache server to serve the HTTP requests, with mod_deflate enabled and configured, the requests for a file.js
will be served a gzip-ed version of it, with a response header telling the user agent that the output is gzip-ed (here, I'm assuming that you enabled gzip compression for *.js files). Therefore, you do not need to change the file extensions of your files.
I'm not sure how you use Gulp.js in your setup since it is a Node.js component and you are asking about Apache configuration.
Also to point out:
Some popular browsers cannot handle compression of all content (http://httpd.apache.org/docs/2.2/mod/mod_deflate.html)