Modern subs do have fathometers, in fact some Nuc boats have one pointing upwards to check for ice. Fathometers are highly directional and low powered, so unless another sub is below the sub it won't hear the ping. Subs also have huge assortments of charts to navigate by for when they can't take soundings.
I think that the sonar operators can tell decern the features of the ocean floor based on the ambient nose and how it echos off the terrain.
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