Yes, I think I have to go with a texture. My idea would be to merge all meshes and unwrap it. As mentioned here I tried to do that but the function doesn’t work. I assume that the algorithm is especially for complex models much more complicated. Is there an algorithm that I can use to get new uv data?
For testing I created a cube with a smart uv with blender. In blender texture painting works fine but in bjs it doesn’t handle it correctly: https://www.babylonjs-playground.com/#9MPPSY#17
I already looked for heatmaps here on this forum but also stackoverflow, threejs, google, etc. I wasn’t able to find anything that could help me.
This would be exactly what I need, but just in 3d space 
heatmap.js : Dynamic Heatmaps for the Web