It's a per-domain limit. So if you own example.com, and you generate 50 different certs for example.com within a week, you'll hit that rate limit. It won't affect your ability to create certs for example.org, though.
It won't affect your ability to renew a cert either. An existing cert for domain0.example.com could be renewed any time (*) even if you created domain1.example.com thru domain50.example.com in the same week.
(*) subject to the 5 duplicates per week rate limit