Currently, people are reluctant to get rid of obsolete interwiki prefixes, because of historical reasons (i.e. they are still used in a lot of pages). See http://lists.wikimedia.org/pipermail/wikitech-l/2014-January/074015.html
A maintenance script should be created to go through the iwlinks table, find all the instances in which the interwiki is used, and edit the pages to replace those interwiki links with external links. Sometimes a template, e.g. [[metawikipedia:Template:w]], is used, so it would be necessary to fix those templates manually, I suppose. Those template pages don't show up in the iwlinks table.
Version: 1.23.0
Severity: enhancement