From a developer standpoint it can be useful to hide document objects from the user when it makes no sense for the user to be manipulating those objects and displaying them would only cause confusion and clutter up the tree view. This does not suggest some nefarious purpose. It could also be more efficient to hide them if there are many of them because then the tree widget is not managing all of those objects, but I haven't tested this.
I make use of this with PDWrapper in the edit placement adjustments dialog. Here the tip tool and tip base are shown as transparent object, which I have called ghosts.
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In the model view they are not shown because the user needs to be editing the Placement Adjustment properties of the PDWrapper object, not directly moving the ghost objects by editing their placement properties.
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But they exist as simple document objects that are removed when the dialog closes or when the user deletes the wrapper object:
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