I found out how to send and reveive arrays of variable length between Emscripten and Java Script, it is totally fine for control data like webMIDI and it is even possible to load and play samples with a length of a few minutes, also loading and saving templates should not be a problem...

Here is a example, it works only with chrome because of webMIDI, and there are some security warnings also because of webMIDI (would be happy to get rid of them...): https://pdsample.handmadeproductions.de/
The size of the Emscripten page is quite big (around 30MB), but it has also more possibilities than for example Webpd or Enzien Heavy.

But I have a problem with loading image data to ofImage() because ofImage():setFromPixels accepts unsigned char const* or const float* arrays, and I only have a lua table with numbers.
I tried to pass the arrays as userdata but without luck. Is there a way to pass the lua numbers into ofImage():setFromPixels(...)? Or to get the array directly from c++ as userdata into setFromPixels(...)?

Now I can answer my own question
Loading an ofImage from a Lua table with pixel values from a .bmp works like that:

ofelia d $0-embindReceiveBitmap;
function embind_6(w, h, buf);
testImage:allocate(w, h, OF_IMAGE_COLOR_ALPHA);
print("bitmap size:", #buf, "bitmap width:", w, "bitmap height:", h);
local count = 0;
for i = 0, h - 1 do;
count = count + w -((w >> 2) << 2);
for j = 0, w - 1 do;
ofPushStyle();
testImage:setColor(j, h - i, ofColor(buf[(i * w + j) * 3 + 54 + count], buf[(i * w + j) * 3 + 55 + count], buf[(i * w + j) * 3 + 56 + count], 200));
ofPopStyle();
end;
end;
testImage:update();
end;

So, now it is possible with Emscripten and Ofelia to load and manipulate .bmp and .wav data in the internet...
And to control the patch with webMIDI (or just Java Script).
And to output (MIDI) data.
I seperated the MIDI and audio example:
https://pdsample.handmadeproductions.de/
https://pdmidi.handmadeproductions.de/
https://github.com/Jonathhhan/ofxOfelia

And I have some ideas and suggestions how to optimize this:

• It would be nice to make a better basic webMIDI Java Script interface template, which is easy to connect to any Emscripten Pure Data Patch.
• It would be really nice if the [ofelia define] object could return a value through the outlet if an embind function is called from C++ / Java Script.
  At the moment the values are banged from a 10ms [metro], which is not optimal...
• it would be great to directly load userdata from java script to Emscripten Ofelia, so the conversion to and from arrays would not be necessary.
• I would like to get rid of the security warnings, that appear because of webMIDI and webAudio...
• Another idea is to have the Ofelia Window fullscreen on a subpage that is controllable from a Java Script interfache on the main page.
• And, because I am not very experienced, it is possible that there are some bad mistakes in my code.
  But I tried my best, and it seems to work.
  Would be nice if somebody more experienced can have a look.

Of course there are some disadvantages compared to a desktop app:

• MIDI is not as tight (but quite good for the internet, still - it could be optimized).
• Loading a picture or a big sound file while audio is running drops the audio.
• It accepts only .bmp images.
• the size is more limited.

I played a bit with shaders and audio spectrum: https://pdspectrum.handmadeproductions.de/

I made some progress, now it is possible to load different formats with https://pdspectrum.handmadeproductions.de/. For images at least: jpg, png, bmp.
For audio at least: wav, mp3. I also found a nice interface library for Java Script: https://nexus-js.github.io/ui/
And I had another Idea: If the interface is completely on the Java Script side it could be simpler and more efficient to just use ofxPd for Emscripten and Pure Data (which already works, but without the Java Script interaction).