Yeah, it would defeat the purpose of a sub if it sent out sonar the whole time to see where it's going. It would light up like a christmas tree on any surface ships' sensors. They probably had old charts or read the charts wrong. Either way, someone's in trouble.
The fact that only one sailor died is testament to the incredible ingineering that goes into these machines. If this was a WW2 era sub, we would never have known what happened to it.