In the Navy's defense, these are fishing trawlers. When they're just idling through the water and the seas are a little rough, they're all but invisible. All of the collisions I'm aware of, the surface craft has been positioned almost directly underneath. Visibility in the open ocean can be hundreds of feet sometimes, so when surfacing, its SOP for the officer of the deck to "spin around" on the attack scope starting well below the surface. Still, this sized hull would be difficult, at best to spot.
I'd guess that the OOD did spot the target prior to collision. Otherwise, we'd have another trawler on the bottom. It takes a little time and effort to change the momentum of 8000 tons of submarine. Yep, Tony, thats one skipper who will be a civilian soon.