Interesting post, RT.
FYI, it is almost certain that sound from transducers is detected in the inner ear, not in the lateral line. The lateral line detects pressure gradients caused by water movement, not sound waves. For a fish to detect the output from a transducer in its lateral line it would have to be very close to the transducer, probably within an inch or two at high power. Beyond that transducers won't move water, that type of energy dissapates very quickly.
People have tried to use sound to repel fish before, with varying degrees of success. Most of the success has been with members of the herring family. No one has had any success with salmon that I'm aware of. The Field & Stream article is interesting but seems pretty weak to me to base any conclusions on. I think the more likely explanation of why the fish at the Wind get put down is all of the boat motors. Motors emit both sound and energy enough to be detected by both the lateral line and the inner ear. Motors put out a lower frequency noise than transducers, which both travels farther and is more easily detected by fishes hearing systems. The noise from the motors and the hulls slapping the water probably dwarfs transducer noise. Then again, maybe the fish get put down by all the cussin' going on. Cheers