There's ports all the way down, and hierarchical means
you are checking at levels below the top so you will see
the ports of lower level blocks checked as the local
network equivalence checks run.
I like to do bottom up LVS, the cells as I create them,
so the top level holds fewer mysteries when I get to that.
The ports on the layout are defined by text labels "attached" to port/pin text layers.
Normally, the ports are defined at the top level only.
There is a command in Calibre (involving "TEXT DEPTH" statement), that tells how many levels of hierarchy down should be used to find the ports (text labels).