Pirates aren't stealing nuclear fuel from operating reactors. It will literally kill them before they get away with it.

They could potentially breach a reactor deliberately but again...why? It would kill them and not achieve anything.

The design for nuclear reactors in commercial shipping has been to use sealed modular units, who's security system would be that attempting to remove or breach would drop the whole unit to the bottom of the ocean where only nation-state level specialized resources could recover it expediently.