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 assets until you expand them (see Expand and collapse assets).
From the Hypergraph Connections editor, you can select all the nodes in an asset at once.
To select all the nodes in an asset
All the nodes in the asset are selected.
In either case, if the asset is in Black Box mode, only published nodes are selected.