Every extension costs money:

• … to keep developers around who know roughly how it works and how to fix it when it breaks, when it needs updating, when there's a security issue;
• … to keep in mind when documenting things, as we have to add yet one more thing to the list of specialist things people may inquire about;
• … to keep in mind when changing things, as we have to work around this, make sure we don't break it, and consider whether we'd need to alter it to compensate; and
• … to run the code, including the (even the code checking whether to run the code is a little bit of a server and user performance cost – to put it bluntly, every page on every wiki is a little slower because we haven't removed this code yet).

After undeploying an extension,

• remove {{OnWikimedia}} from https://www.mediawiki.org/wiki/Extension:NameOfExtension
• remove entry from https://www.mediawiki.org/wiki/Developers/Maintainers#MediaWiki_extensions_deployed_by_WMF