dunno if you managed to resolve your problem in the meantime,
but I had a similar error (under macOS and emscripten 1.39.17):
After downloading and installing everything, I ran emsdk_env (which should generate the ~/.emscripten file in the user folder, if I remember correctly)
But it seems, that Qt Creator could not resolve the var for the defined emsdk_path
emsdk_path = os.path.dirname(os.environ.get('EM_CONFIG')).replace('\\', '/')
so I replaced all the placeholder with the explicit path:
emsdk_path = '/Users/myuser/Documents/Programming/emsdk'
I also added
COMPILER_ENGINE = NODE_JS
JS_ENGINES = [NODE_JS]
at the bottom (not sure though if that was needed)
After restarting Qt creator the compiler and toolkit for WebAssembly wer successfully recognized.