I thought maybe it is a good idea to collect Emscripten behavior / bugs that differ from Ofelia without Emscripten.

Five things for now:

[cos~] does not work, [expr~ cos(2 * 3.14159 * $v1)] does.
[array] does not work, but [array define] does.
ofSetLineWidth() does not work.
I need to set the ticksPerBuffer in ofApp.cpp from 8 to between 16 and 64, depending on the complexity of the patch and the power of the computer for avoiding audio glitches and artifacts (maybe there is a way to optimize it).
Shader need to be ported from GLSL to GLES or directly written in GLES.

If using webgl2 you need to edit the compiled .js file.
search for:

var ctx = canvas.getContext("webgl", webGLContextAttributes);

and change it to:

var ctx = canvas.getContext("webgl2", webGLContextAttributes);

Maybe it is also solvable with an Emscripten compile flag or with editing the file library_webgl.js in the emsdk directory.
Edit: Not necessary anymore after the changes I made.

In https://github.com/openframeworks/openFrameworks/blob/master/addons/ofxEmscripten/libs/html5audio/lib/emscripten/library_html5audio.js replace:

var context = new AudioContext;

with:

var context = new AudioContext({
            latencyHint: "interactive",
            sampleRate: 44100
});

Or whatever sample rate you have choosen for your project. This will prevent playing the sound with the wrong tempo and pitch (if the sample rate from the sound card is different from the project sample rate). latencyHint: "interactive" is not really neccessary, because it is the default.

The [midiout] object does not seem to work with Emscripten.
And