I tested locally and deleting MediaWiki:Common.css removed the <link> for 'site.styles' module from pages.
Make sure that you're not actually viewing cached page HTML that still has it.
Also make sure that you're not using the other MediaWiki pages that are included in this module: MediaWiki:Print.css and MediaWiki:Vector.css (or MediaWiki:Monobook.css, etc., depending on the skin).
If you still see this behavior and want to try debugging it, start in ResourceLoaderWikiModule::isKnownEmpty() and its callers, this is the method that decides whether the <link> will be generated.