The rate limit is a sliding window. You can issue a certificate as long as you haven’t issued 20 certificates for the same domain in the past 7 days. So if you issue one every hour today, you’ll hit the rate limit after the 20th, then 7 days after you created the first one you can create one more, then an hour later one more, and so on.
(I thought this was explained in the rate limit documentation, but reading it again now, I can’t find it…)
BTW, you could just issue a single certificate for all 40 subdomains (up to 100 in fact) and it would only count as 1 towards the rate limit.
This script is helpful in figuring out when you’ll be able to issue again: