Will this "data-out.conf" find the cloud ES instance by checking against main "logstash.conf"?
I assume you mean .yml, not .conf ? (if so...)
The Elasticsearch settings in logstash.yml are only applicable to monitoring, management, and modules. You still have to define your hosts (and credentials if needed) in the output { section of your configuration [1].
If have 1 instance/cluster of Elasticsearch , it does become a bit redundant to redefine the same connection everywhere. Also note, the output { section does not currently allow for a cloud_id , you will need to use the host name(s) directly.
[1]