Emscriptem doesn't generate C/C++ code, it generates Javascript, which then runs on top of a Javascript execution environment (V8 etc).
The real comparison would be some C/C++ code run though this and running in Javascript vs handwritten Javascript.
(It's possible what you mean is a comparison of the generated machine code from LLVM vs that from the Javascript engine. I agree that would be interesting, but I think you'd be better off comparing the machine code generated by a Javascript-on-LLVM implementation such as http://github.com/omo/jsllc vs that generated by a conventional Javascript runtime.)
FWIW, the author did somewhat touch on the issue of performance at the end of the article: Of course speed is an issue here. Emscriptened benchmarks currently run at about 1/20th the speed of gcc -O0 run on the original C++. and goes on to explain where the performance loss comes from.
To be honest, I'd use GWT (http://code.google.com/webtoolkit/overview.html) for this kind of thing. Does the same thing, only it's Java -> Javascript. Been around for four years now, and hell, it's Google. Their documentation is excellent, for a start.
If I weren't so comfortable in Java, though, I'd definitely think about using this.
Actually there is, I can't remember the name right now but there is a 3D engine build in Java (it runs on top of OpenGl, but that is just used to draw and interact with the graphic card).
It'd be interesting to see how decent performance can get between the LLVM optimizations and the tracing/JIT of the newer JS engines.