It seems likely that Logic just doesn't know where to look for those libraries. The simplest way to fix this, if I recall it right, is to navigate to where the Apple Loops library is located in Finder, then drag 'n drop the folder from Finder into the Loops tab in Logic.
As far as additional content, I've never added any of those to the library as a.) the Apple Loops library may have additional metadata that allows them to be searchable in the Loops browser; and b.) the Apple Loops library uses a different file format: .CAF rather than .WAV and .aiff. I think there might be a way to convert the files to the .CAF format, but I don't know what it is. I do know it's not as simple as just dragging and dropping the directory where those loops are kept into the Loops browser.