I've am not familiar with nor ever used multisite or Multi-Network but found this which might be what you are looking for. Their readme says
The plugin is fully compatible with Multisite and Multinetwork. In a Multisite it will take care of generating the certificate for all sites in the network. In a Multinetwork you will additionally have the option to generate the certificate for all sites in all networks.
Excellent, so glad I could help. So glad you love my photo’s, been busy
with a major update to my site (5 months now) that’s fallen by the way side
as I have thousands of images to still get up there, just never enough time
in my days.
Enjoy your new SSL Multi-Network, it’s so nice to see how many people are
writing plugins and scripts for Let’s Encrypt which is why it is already
taking the world by storm.