You can select encapsulated nodes by selecting them in the scene panel, Outliner, or Hypergraph. In the Hypergraph Connections editor, encapsulated nodes will be hidden in their respective containers until you expand the container (see Expand and collapse containers).
From the Hypergraph Connections editor, you can select all the nodes in a container at once.
To select all the nodes in a container
In either case, if the container is in Black Box mode, only published nodes are selected.