That's correct - you can get up to 50 new certificates per registered domain per week. If you have just 5 subdomains for each registered domain you are unlikely to run into this limit at all.
(If you have reached the limit you can't get any new certificates until the first one rolls out of the sliding window, but you can still renew your existing certificates).
If you are planning to obtain thousands of certificates in a batch, you are more likely to run into the "New Orders" limit of 300 per 3 hours, per account.