Registrations don't cause a lot of load. They're essentially just one row in a table.
Certificates have to be signed by a Hardware Security Module with limited capacity. OCSP messages have to be signed every couple of days for the lifetime of a cert by the same HSM. This is significantly harder (and more expensive) to scale.
Weird, why allow a generous 500 registrations per 3 hours, while limiting certs per domain like this? Anyone have a link to anywhere that letsencrypt explains what they are trying to do here?