With invalid bookmarks no longer being removed (#47 (closed)), it would be beneficial to still show them in the Shortcuts pane and Bookmarks menu. As the paths are invalid, the entries would be disabled in the pane or menu, but ideally the path should still appear in the tooltip or statusbar.
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Like you already noticed below, it looks like your current thunar version is a bit outdated and still has bookmarks and go menu mixed in one menu item. In the current master, thunar_window_update_bookmarks_menu will create the bookmarks menu item.
Probably you are using some older version of thunar. The separate bookmarks menu-item was introduced in thunar 4.17.7 or 4.17.8. If you are planning to develop on thunar yourself, you anyhow will need the latest master. Here some basic info for building thunar: https://wiki.xfce.org/thunar/dev/build_and_run
Shortcuts are stored in ~/.config/Thunar/accels.scm. Bookmarks as well can have shortcuts (currently a md5 is used to identify them ... see #295). The actual bookmarks are stored in ~/.config/gtk-3.0/bookmarks (same forall gtk applications)