I can't begin building my WPMU server until this evening so I thought I would ask the question here to see if anyone has experience with this scenario.
Setting up a WordPress Multisite with Lets Encrypt SSL. Using Sub-directories.
I just want to ensure there is no issue with Common Name or something similar.
SSL Certificates have nothing to do with sub-directories, thus it will not matter. The Common Name in SSL identifies the host (Eg. www.example.com).
If you are using sub-domains it would still be easy to accomplish.
The example below will generate a single certificate for example.com, www.example.com, en.example.com and fr.example.com.
In your nginx site configuration, you will specify the single certificate which will be valid for all the domains yous specified with certbot.