There are two ways to delete objects. The preferred method is by managing the object itself. The less-preferred method is to do so by managing the object's parent collection (or parent newspaper/book).
The object and any of its children (if applicable) will be removed.
Another way to delete an object is to do so via the Collection tab when managing its parent collection. If the object you're deleting has children (e.g. if it is a newspaper issue, book, compound object, collection, etc.), those children will not be deleted.
We recently discovered a bug in Islandora's handling of newspapers: even if you delete the Newspaper via its Properties screen, the Pages of its Issues will become orphans. Please use the Islandora Orphaned Objects module to purge any orphans you might have created after deleting a newspaper.