I would like an axiom that states that some APs such as IAO_0000115 (definition) should only appear once per class.

This is of course impossible in OWL-DL - we would rely on external code or non-DL rules engines to enforce.

If we do not wish to globally restrict on a per-property basis, this could be done on a per-ontology basis. E.g

Ontology(go.owl Annotation(IAO:has_maximum_one_per_class IAO_0000115) ... )