Emscripten used to use Java for Closure Compiler minification, but no longer does since there are (AOT compiled Java) binaries available for it, for all major platforms. It fetches them using npm. So that part of your post is a little out of date.
(As to why use Java at all, Closure is written in it, and its advanced optimizations make a huge difference!)
The use of both node and python in Emscripten is slightly redundant. When Emscripten started, node could not yet replace python for what we do with it. Today, if someone wants to refactor that code to node we'd definitely be interested in such a PR! But overall such a refactoring has been lower in priority compared to other work (new wasm features, performance, etc.).
Or Java for minification instead to npm based tooling for the same purpose?