How does Google's native client (both NaCl and PNaCl) compare to Emscripten in ported C++ code performance?
The best way to find out is to port something and profile. I have done work with both systems, porting CPU-intensive C/C++ libraries to both NaCl and JS-via-Emscripten. I have found both to be remarkably performant. Not exactly the same as compiled C/C++, but fast enough that they can accomplish their tasks in real-time.