Some updates will be available in nazca >0.5.13 to add or hide stubs after cell creation (in closed cells).
The put_stub function has been ported as a Cell method, hence, you can now also say
C.put_stub() where you use
nd.put_stub(). Along this path you can add stubs as
cellA.put_stub() after the cell is closed; By exception, as normally you will get (a desired) Python Exception when connecting to a closed cell directly (in a circuit you would connect to an instance of the cell, not the cell itself). Still, it is advised not to add stubs after cell closure, because such changes will not be reflected in the bounding box of the cell, which may even lead to netlist errors when stubs/pins are placed outside the bbox.
Better is to place all the stubs you may want to visualize inside the cell during cell creation, as would be the normal situation. Then use the new cell method
hide_stub(), which will exclude stubs and their annotation from export; The hide_stub method will be allowed to operate on closed cells.
An other way to hide stubs, also used in Nazca PDKs, is placing them in logical layers and just switch them off in the layer view. This will affect all stubs at once, and not a selected few though.