This is very cool. You can basically even call all Java classes (and the other way around) from that JavaScript! (And reliably limit the classes that can be used if you want to execute JS in a safe environment.) Why isn't this used more often? (Or is it used more often?)
I can't speak to whether it is used more often, but I would bet the java-based Nashorn vm is significantly slower than the c++-based nodejs. In fact, a cursory google search shows this is the case, and it's not even close.
While it is of course going to be slower, "it's not even close" is a judgement claim. The tests you have link talk about 1.6-2-3 times the difference. In a lot of applications the performance hit is going to be worth gaining access to the whole Java ecosystem of libraries.
Also the performance is very likely to increase with newer versions.
Nashorn isn't that slow, but there's another JS-on-the-JVM project called Graal.js which is about as fast as NodeJS/V8.
One reason Nashorn isn't used that much is that it doesn't expose a node.js compatible API. JS people often want Node specifically, not just the ability to run JS. It has some cool features though. The shell mode is neat.
For those who don't know the JVM comes with a JavaScript engine by default: http://www.oracle.com/technetwork/articles/java/jf14-nashorn.... And you can even get v8/nodejs to be compiled in your java jar binary: https://github.com/eclipsesource/J2V8