How does one add references to tables and diagrams included in a Pages document?
You can add a bookmark at the position of the cursor with Insert>Bookmark. Bookmarks can be managed and renamed in Document(top right corner)>Bookmarks. You can then highlight any word(s) and add a link to a bookmark with Insert>Link>Bookmark. This will add a hyperlink to the bookmark.

Unfortunately, in Pages you cannot bookmark a table or footnote. You can, however, add a bookmark to the cursor position left to a table, so it will practically link to the table.
This does not work for footnotes, though. But if you use the same source multiple times you should also reference it multiple times in its own footnote, instead of pointing to another footnote, anyway. Since you may reference the same source in multiple places in your document, outgoing links from the bibliography to the footnote don‘t make sense, because you only list each source once in the bibliography which makes it impossible to link to multiple footnotes.

EDIT: But you can add links in footnotes that point to a bookmark in the bibliography.