./users roles adminuser -r superuser
When running the roles sub-command a -r is a remove option.
The command you ran remove the superuser role from adminuser.
You can see the help text for by running
bin/x-pack/users roles --help
With respect to your other questions:
No, users are only created in Elasticsearch. The other products in the Elastic Stack use Elasticsearch as their user store where applicable. However, you will need to configure those products so that they can authenticate to Elasticsearch.
Please see: Logstash Reference [8.11] | Elastic