Auto-links are a front-end UI feature and aren't actually stored in the database. Links have to be created in order to save them and find them for tracking. Otherwise, every word and combination of words is a potential auto-link.
I'm sure you've noticed if I talk about the wiki or how to give an article a category or that we have an XF demo site, there are numerous auto-links to completely unrelated articles to what I just said. When new pages are created, those terms get auto-linked in other posts. But as those posts don't get saved again, the links won't be updated.
In VaultWiki 4, we no longer track links that don't originate from within a wiki article. Without a properly structured DM (as only the wiki DMs are), the link data was typically unreliable in VaultWiki 3. Without this, there were nearly 100 extra plugins just to handle adding and removing links (poorly), and in some content-types it was not possible all all due to other design issues within vBulletin itself. The cost of that many plugins (under vB 4 and lower anyway) was not negligible. And since the data was rarely trustworthy, it was better just to do away with the feature.