This does not really help.
When i start a new project, i need a certificate with the new subdomain in it. This means, i need a new certificate, independend from if i want to add a domain to the common certificate or if i want a certificate just for the new subdomain. So i would now need to request a new cert for the new subdomain now, and at the next renewal time i need to remember to add the new subdomain to the common certificate.
But both do not really help, when i hit the API limit and want now to add a new subdomain (either as single cert or as new common cert with one subdomain more), which will only work after 60 days. Which effectively means, that my new project is for 60 days only available unencrypted.
And on the other hand, it may be not wanted to have all subdomains on the same cert.
It is also impractical for independend configuration of the subdomains.
For example i use a configuration for my webserver, where i can do
touch sites/newdomain and the needed stuff (webroot, log directory, server configuration) is created on reload of the webserver. I thought about adding "add letsencrypt certificate" there, but this will not work with the limit.
I see the point in some limit, but i think it should be like 50-100. Who needs more than 100 subdomains may want to buy a wildcard certificate somewhere anyway. But a moderate number of subdomains should be possible. So better a global domain limit than a subdomains-per-domain limit. It should not make any difference, if i sign 100 domains or 100 subdomains.