Let’s Encrypt currently doesn’t support wildcard subdomains. They plan on adding this feature in January 2018:
So, at the moment, you would probably have to register each subdomain individually with LE and then you should be able to use SSL on those subdomains when properly configured.
For more info, you should search on the wordpress.org/support forums or Google since CBOX is just a WordPress plugin and WordPress handles the multisite portion of what you are asking for.
Thanks, Ray. I’d seen that LE didn’t support wildcard subdomains but hadn’t caught the announcement that support is coming in January. Good to know.
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