The visualization of point sets in PointSetVtkMapper2D is currently defined in terms of its spatial extent through the renderer-dependent properties "point 2D size" and "Pointset.2D.distance to plane". That means that, when zooming in very far, these markers will become too big to be practical:
I propose to add a setting to the PointSetVtkMapper2D class that changes the behavior to a fixed size (in pixels) on the screen through an additional property "Pointset.2D.fixed size on screen".
I've prepared a patch that would add the desired result as a feature while not interfering with current behavior.