Yes, I was bitten by this domain rate limit during renewal last week. Having requested 5 certificates for subdomains in December I had to rerequest new certificates. Two or three days before this I requested a new 6th subdomain cert (for another virtual machine) and was only able to renew 4 certs until the 7 days where over. This was unexpected.
This made me change my renewal policy to 30 days instead of 15 days not to have expiring certificates because of this limitation.
What the reason for this limit? Or maybe someone has at least a use case for this? I am not sure whats the difference between 100 different names in a single cert and 100 different certs with a single name each. Especially compared to the very high limits of 500 request per IP per 3h for example I don’t see this limits on subdomains protects the LE Infrastructure at all.