Ships are not currently inspected at sea, and it's impractical to do so. The cargo is in giant stacks, and you need a dock to unload it for inspection.

Finding it at the dock is completely useless. You can set the nuke off while still at sea and still destroy half a city.

There is no mechanism for interception of such an attack at the moment.

You need a neutron detector, rather than a Geiger counter, for nuclear material detection by the way.