Rigger 3 shows how many crew are needed to run any size ship (hull^2 + 3 I think). What I don't remember is weather there is a good example of a cargo frighter in the book so you may have to make up stats.

Anyway take the number you get from the book and multiply it by 1.5 to represent the night shift as well, if the ship is at dock the double the number again for loaders, customs officals, safety inspectors and so on.

In real life the hardest parts of a nuclear weapon to aquire are the Fissionable/Fussionable material and the tools to machine the material properly. Detonators and electronics will be (relatively) easy to get. So depending on what exactly is in this ship of yours I'd say anywhere from 1-3 Zombies on guard.

Gee, I hope the runners make it OK