The most complicated part is to properly craft the OpenSSL command to properly get you SSL certificate to be signed, but if you use Lets Encrypt, I guess it easier then... I answer an other thread recently with the command that I had use for multiple subdomain certificate, that I had work an lot of time to work around the issue existing at the time with OpenSSL as there were some kind of bug that wasn't fix for a long time...
In uwsgi, you mostly go there only to tweak the config for performance...
If you use only one certificate for multiple subdomain and you are not the only one using the sites, I guess you better read about how manage security related to such kind of deployment.
Richard