Possibly. Whether a state can require an unregistered business to stop operating depends on the type of business, the registration or licensing requirements involved, and the laws in your jurisdiction. Some businesses may be given an opportunity to correct registration issues, while others may face restrictions or enforcement actions until they comply.
Operating without proper registration does not automatically mean a business will be shut down. However, failing to meet legal requirements can lead to government action (such as administrative fines, suspension or revocation of licenses or registrations, cease-and-desist orders, administrative dissolution, injunctions, or other remedies authorized by law) if the issue is not resolved.
Whether a business may actually be ordered to stop operating depends on the applicable statutory authority and the specific facts.