Yes. Who cares if your file looks "messy"? When you are delivering any content to users, it should be as minimal as possible. You, as the developer, aren't reading the compressed files. They should be compressed automatically as part of your deployment cycle. If you don't have this automated, then include it in your manual process. Develop normally locally, but before you push stuff out run it through a compressor.

Also, I recommend the Google Closure compiler instead of jscompress. Just leave it set at simple unless you are explicitly using Closure. http://closure-compiler.appspot.com/home