Most ACME clients register an account the first time you run them, and then reuse it afterwards. If you use a typical client, and follow its documentation, it won’t be a problem.
Issuing 1000 certificates may take you 10 hours, though.
For users of the ACME v2 API you can create a maximum of 300 New Orders per account per 3 hours.
You should read the links posted before, as well as: