Drupal configuration is normally changed or removed through the configuration import and export process. For example, the process I follow is to make the change in the configuration locally, export the configuration into the source code, deploy the source code to a remote server and import the configuration. Using this mechanism, configuration changes that were exported locally are imported into the site and are ready to use.
There are certain situations where using update hooks to update the configuration is necessary. This means that you would change the configuration in your system directly using code in update hooks, rather than following the export and import process. These situations are rare, but necessary from time to time in order to maintain a consistent configuration on your site.