From the docs about wp plugin delete:
Deletes plugin files without deactivating or uninstalling.
so after runing the comand on a plugin I would expect the admin plugin page showing the warning about the missing plugin being deactivated and all the uninstalling database related actions have not taken place.
Just run uninstall with the --deactivate option and you are done.
https://developer.wordpress.org/cli/commands/plugin/delete
https://developer.wordpress.org/cli/commands/plugin/uninstall/