Currently, any subcomposition you create gets added to the Node Library. This is good for general-purpose subcompositions that are meant to be used by many compositions.
But for subcompositions that you only intend to use in one composition, it would be better to keep them with that composition, and not have them appear in the Node Library for every composition. These subcompositions could be stored with the parent composition and only appear in the Node Library when editing that composition.
This would also make it easier to share compositions or move them from one computer to another, since you wouldn't have to track down all the dependent subcompositions.