I don't see why the language the tool is written in matters. Lots of NPM modules have native C dependencies and it works fine.
Closure advanced mode will do a lot better than 5% compared with Uglify.
Closure advanced mode will do a lot better than 5% compared with Uglify.
That said, closure being in JavaScript has more to do with choosing rhino than anything else. If you were starting a project like closure today you wouldn't use Java.
Re: advanced mode, totally depends on what kind of code you've got. Lots of inlineable functions and constants? Double digits easily. Lots of objects and DOM? 5% better than uglify is optimistic.
It should be rather trivial to have a gulp/grunt task that installs Java and runs CC. CC could even be packaged as a EXE if desired.