Not really.
Yes! But only if you are a long way off, listening to the sides or off the stern of the approaching merchant ship. This one, at 51,000 tons, is fairly small, and so has relatively less mass and cargo spaces and voids between the engine room (noise source) and the bow of the cargo ship.
A bigger one, (100,000 tons to 250,000) tons are actually very, very quiet when you are just trying to listen to their engine noise while your submarine is front of the bow.
Very true. Someone definitely screwed up big time. However this incident occurred 25 miles south of Cape Ashizuri which is the middle of the Bungo Suido. That's the nautical equivalent of the middle of a super highway, so relying on passive sonar is problematic due to the sheer volume of shipping traffic in the area. Why they didn't surface outside of the shipping channel and then proceed into the lane on the surface is beyond me.