What makes you think they hadn't seen them? I'm pretty sure they had seen them, they were an experienced and capable crew. They just thought the route was safe and that they were low lying islands.
Mainly because they weren't mentioned before they got over them and because the reaction seemed from the transcript to be one of surprise.
And I'm sure their SOPs would also advocate not to overfly radar contacts at low level unless you can visually ID them. Remember, no NVD on this aircraft.
DB, you are pre-empting the investigation with a guilty charge based on limited information - not really fair?