I did a some more research on your question and there's one more step to getting your sub libraries content items. Your sub-libraries are not treated as libraries at all, but are actually organizational folders within your library. For example:
Only Library 1 and Library 2 are considered libraries. SubLibrary 1, SubLibrary 2, etc... are considered folders within each library.
Take a look at the following documentation, especially item #3, for more info on how to get sub folders and sub items.
Here's a quick sample of how you could do it in a foreach loop, though.
foreach(var library in documentLibraries)
var childItemsUnderFolder = librariesManager.GetChildFolders(library);
foreach (var subLibrary in childItemsUnderFolder)
var subLibraryItems = librariesManager.GetAncestorItems(subLibrary);
From there you will probably have to construct your own libraries and library items list to make it all manageable in your view.
Take a look at this forum post about how to get associated taxonomies from a document.
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