I'm working in PhpStorm 2016.1, on Mac OS X. Colleagues who are on Windows have in Tools tab a Deployment menu. I've got nothing...
Same in Preferences > Build, Execution & Deployment -- all I've got is Debugger and Coverage.
Make sure that "Remote Hosts Access" plugin is enabled in Preferences | Plugins.
That's the only reason why "Deployment" menu would not be available to you.