Since 1.39, the installer will warn about the use of deprecated settings. But this only works as long as the declaration of the config setting is kept. Since people often upgrade from old versions after many years, it seems useful to keep the declaration around for a long time.
The old setting can however be ignored. The deprecation warning can just say that the setting no longer works. We just need to declaration in place so the installer tells the user.
Maybe instead of using the "deprecated" flag in the schema, we should have an "obsolete" flag for settings that are no longer supported? We could keep them indefinitly.