Get Real
It worries me that you've misunderstood the municipal/international law/UNCLOS/maritime law/ports question so much.
Think about this. I think that you will agree with me that Paphos, Larnaka and Limassol are all places within Cyprus. Yes ? You'll also agree with me that these places all have ports or harbours of some kind or other. Yes ? You'll also agree with me that these ports and harbours are, by definition, within the jurisdiction of Cyprus. Yes ? And you'll also agree with me that the laws of Cyprus apply within these ports and harbours. Yes ?
If yes to the above, then we are agreed that Paphos, Larnaka and Limassol are all within Cyprus territorial waters, i.e, within RoC jurisdiction. Yes ? So we agree that the municipal law of Cyprus covers these ports and harbours. Yes ?
Further, by definition, these ports and harbours are not outside Cyprus territorial waters and they are not in the 'high seas'. Agreed ? Agreed. Therefore the regulation of ports is a domestic, municipal, matter. It is not a matter of international law.
Where does various maritime law and UNCLOS etc come in then ? As I said in an earlier post, these are treaty instruments whose primary concern have been international shipping safety (hence concern for meaning of innocent passage, SOLAS (saving of lives at sea), environmental protection, exploitation rights, zoning and demarcation, and so on. They are necessarily international matters because one is dealing with movement across and between different jurisdictions.