Full R-C extraction is iffy at best for a hierarchical design. The original code was written assuming a flat layout, and I have done some work to allow it to work in a hierarchical context, but there's a lot of work to be done, and meanwhile it does do things like output "null" nets.
The question of when a subcell gets an additional port: Whenever magic detects something connected to a net in a subcircuit that is not declared a port. Doing parasitic capacitance extraction will often find lots of coupling between parent cell and subcell, which may cause it to add pins so that the parasitic cap has something to connect to. If you extract without parasitics, you will only get extra pins if something is really electrically connected to a net in a subcircuit that is not already marked as a port.