I wish to disallow search robots to gain access to the whole domain including subdomains using Robots.txt and potentially .htaccess
I wish to make certain that any new subdomains later on are blocked without needing to create one out of the main of subdomain each time.
If you wish to block robots via robots.txt, you will need to create one for every subdomain. I would recommend a script that monitors your Zone File after which instantly produces one.
Another solution is by using HTTP Basic Auth. It'll block all bots from being able to access the CNAMEs but it'll require customers to go in a account information.
Or you might use IP Tables to limit access by IP range.
You will find multiple solutions will prevent robots from being able to access your CNAMEs, and you will find much more methods to prevent search engines like google from adding your website to their index.
It'll rely on whether who you need to let in (good bots, bad bots, customers, etc.) which will figure out what solutions you would employ.