Aren't all of the proposed routes for supersonic planes over oceans?
So "just" flying at super sonic speeds over oceans seems like it could be a disaster for marine life. The disruption to whales from noise pollution comes to mind
But not transferring from the air to the ocean, the phase transition attenuates sound a great deal.
It's things like propeller noise and sonar which are causing problems. A sonic boom over the ocean is not going to ruin any whale's day, short of perhaps alarming them when they come up for air.