Of course. Your schematic must fully comply with the layout. DRC will go well and without adding these elements, because this procedure only checks your topology, the correctness of the technological distances. LVS (Layout versus schematic) checks the compliance of the layout to schematics.
"Pruning" rules might take out properly tied off dummies,
but schematically representing what you laid out, as you
laid it out, has no such dependencies.