By selecting or clearing the visibility check box and setting a color on the Global layer, you control the display of these types of holes:

The display of non-through-hole vias depends on the display status of the layer on which they reside. You can control the display of holes for vias and pins separately. The display of groups may also depend on the status of the layers. When a group is marked visible, all of its members are visible. When a group is marked hidden, the display of its members is controlled by the visibility of the layers where the members reside.