I create a circle with angle1=0 and angle2=0, so nothing is drawn but in the XML is a line
<arc angle1="0" angle2="0" id="7" radius="12" center="6" type="simple"/>
which i cannot delete (except by editing the XML) because i cannot select it with the mouse.
In consequence of this i cannot delete the center point of the zombie circle because it is burdened with a dependency. As the dependency chain can be arbitrary long, an arbitrary number of objects cannot be deleted.
Propositions with falling precedence:
Show some visible handle for invisible or extremely small objects, like the little circle or the label for point objects. In case two or more handles have same position, clicking with mouse selects any of them; <Tab>-key selects the next handle on same position.
In tool options, add a list "list of dependend objects". This is was most spreadsheet apps offer as 'show dependend cells'. Clicking on a list entry jumps to this object. Even a second list "objects this object depends on" could be helpful.
Instead of graying out the 'delete'-function in context-menu, ask user "Delete all dependencies also?"
Create a tree-like view of all dependencies, where i can select/edit/delete every object. Because some objects may depend on two or more others, this eventually is not a tree but a mesh.