Pointless to bet because if they announce there was nothing unusual about the ship and let it go on its way, you'll simply insist they DID find something and covered it up in order not to panic the public.
Nuclear bombs, at least ours, do not emit much of anything (been there, done that). They would not make their surroundings radioactive unless they were left in one place for a very long time.
Crude nukes, or dirty bombs, might be a different story. However, even these could be shielded. It seems likely that anyone that could make 'em could also figure out how to make 'em hard to detect. Shielding would be the easy part.
'Course, one of our advantages is that so many of the bad guys aren't exactly the sharpest knives in the drawer...