Let's Encrypt currently enforces the following rate limits:
"Certificates per Domain" is defined as "Top Level Domain + Domain (a 'registered domain')", so certificates for www.example.com, foo.example.com etc. would all count towards the rate limit of example.com.
Let's Encrypt supports SAN certificates (i.e. ones with multiple domains or multiple subdomains) with up to 100 DNS names per certificate. You can also generate one certificate per domain (or subdomain) if you wish to.
It should be noted that Let's Encrypt has issued about 200,000 certificates total so far, so this would be a significant increase in load if you're planning to get those certificates issued in a small window of time.