In my understanding, Ender is a command line tool that helps organize your javascript dependencies. We can use ender build underscore qwery to produce a ender.js file which contains the codes of underscore and qwery, then we can include this file in our html.
However, I noticed that ender gets those libs from npm site, so I'm worrying that if all of those libraries could be use in browser side?
Ender.js is a tool for JavaScript dependency management in the browser.
It uses npm for the underlying package management (basically to fetch packages), then compiles all of these fetched packages into a single minified file, that can be used by the browser.
The fact that npm is used does not mean that the packages are (only) for node. Most of them are browser-only, some of them can be used by node and the browser. Basically, there is nothing to worry about.