You can fly subsonic over land and go supersonic over oceans. That would make a trip to Japan much faster! And won't impact humans living underneath the flight path (since it won't go supersonic until it's over the ocean)
Flights these days often aren't even traveling close to the speed of sound, so there's room to design a plane more efficient at that speed as well.
Assuming it has the range. Trans-Atlantic is IMO not that interesting. You can already get to London from the East Coast same day. The continent is mostly a red-eye but that's OK in lie-flat business class. Even comfortable trans-Pacific is a slog but that takes a lot of range.
A supersonic airframe is typically inefficient at subsonic speeds.
2. If you're flying NYC-London or LAX-Tokyo, the portion you spend over land isn't a big contributor to the overall efficiency.
As someone who grew up hearing sonic booms all the time this is very puzzling to me. I keep seeing mentions of how the sonic boom is such a huge issue... really?
I can't help but imagine people used to think about these things, but they haven't for a while. I remember checking what was on the in-flight radio ~8 years ago to hear "Love when you hit the ground, girl."