The visibility of the ElumTools Calculation Point family instances can be controlled using all of the same methods as a typical Revit element (visibility/graphics, hide command, worksets, and more).
If you are unable to see the family instances using Revit's visibility settings, the reason typically has to do with the View Range parameters. When ElumTools places the calculation family into the model, it tries to choose a Z-coordinate such that the family will be visible in both ceiling plans and floor plans.
With a few exceptions, this usually means the family will be placed based on the View Range parameters of the View that was used to add the points. Typically the family instance will be placed at the "Top-Plane", if placed in a Floor Plan, or the "Cut-Plane" if placed in a Ceiling Plan.
Note that you can move the calc points family, if it doesn’t get placed in a good location by default. The only requirement is that the family instance be contained within the space of interest (otherwise the points are not considered when you calculate).