If there are sub layers with objects under a top level “parent” layer without objects, the top level layer will not show anything selected if you select “by layer“ and specify this top level layer. Also this top level layer will show up if you filter for empty layers. But if you try to delete it Rhino will warn you there are objects on the sub layers. If you look closely at the warning though it will list the sub layer by name, and ask if you want to delete the sub layer and the objects on it.
I suggest you try “purge” to clean up the empty layers as this way Rhino will recognize the objects on sub layers and you can avoid the nuisance of confirming you don’t want to delete any layer with objects.