Point clouds are just another type of 3D object, so you should be able to safely put them in an instance master, and have them show up in the instances.

This ICE tree adds a point for each person in the instance master. Here I added some spheres, but I could just of easily instanced some geometry and put a halo over everyone’s head.

If the instance master model is not at (0 0 0), then when I parent the point cloud to the model, the point cloud gets a local pos offset. So, I can either manually reset the local pt cloud pos to 0 0 0, or handle it in the ICE tree (by undoing the local pos offset by multiplying by the inverse transfo matrix).