Hello Richard,
each component can have its own configuration. I think the configuration of a component is treated as a subobject so the component configuration of different components may have the same name. But there is no use in assigning a component a configuration which is not existing. So it is either an error or someone deleted the component configurations and forgot to cleanup the application configuration.
The only special thing I remember when it comes to web dynpro configuration is in the settings for web dynpro applications using the floor plan manager Framework e.g. Requisition maintenance. Due to the way these applications were implemented for eRec it is important that all usages of views of a certain component get the same configuration assigned even if a certain view was not adjusted. Otherwise the floor plan manager framework will create 2 runtime instances of the component which causes trouble.
Kind Regards
Roman