Currently, namespaceDupes.php checks only the namespace and title columns of the page, pagelinks, templatelinks, and redirect tables. It does not currently check the linktarget table and will need to be updated for the links migration.
According to wikitech:Backport windows/Deployers, "When a new namespace is added to an existing [Wikimedia] wiki, the namespaceDupes maintenance script should be run for that wiki." This has been done several times since the start of the links migration. While it's possible that in some cases there may have been template link targets that the script failed to properly update, the bigger issue is that once the tl_namespace and tl_title columns are dropped, the script will fail with a database query error before it even starts checking the pagelinks table for the prefixes corresponding to the newly added namespace.