In this page:
It's not clear what will happen when my account hit the 50-per-week limit for sub-domains.
Does all the account will be limit from that point, or only the top domains of those sub-domains?
Can I still order new SSLs for other domains name?
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.
Adding on to danb35 comment ...
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
domain50.example.com in the same week.
(*) subject to the 5 duplicates per week rate limit
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