I have nginx fronting around 15 different (very low traffic) websites (most static, a few python), all of which have Let's Encrypt certs. The required additions to the nginx conf were minimal and easy. Adding a new subdomain is trivial. Fetching the initial certificate from Let's Encrypt is a short, easy command line. And "sudo certbot renew; sudo /etc/init.d/nginx reload" in a cron job keeps the certs up to date (the "renew" command is smart enough to go through the list of certs you have and renew them all).

It's really hard to imagine it getting much easier.