I might be missing something with your comment, but there are obviously animals that live in and around 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

Noise pollution in oceans is a serious concern, yes.

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.