Does a vessel with american vessel registration have to be registered in North Carolina?

Yes, it does. Coast Guard documented vessels that have been in North Carolina for more than 90 consecutive days must be registered.

That said, according to the North Carolina Wildlife Resources Commission, “federal law restricts states from issuing titles for documented vessels since the USCG issues a Certificate of Documentation (COD) to owners of documented vessels which supersede a state title. To register your documented vessel (in the state of North Carolina) you will need to submit the following:

A Completed VL-1 Form (link to PDF here).
A copy of your Certificate of Documentation. DO NOT send the original. That should be kept for your records.
Appropriate fee for registration only.

USCG Documented vessels can be registered for a period of 1 or 3 years but cannot be titled. You may register your vessel by mail or in person at a local (North Carolina) Wildlife Service Agent.

To apply for initial vessel documentation, click here.