As an air-burst, yes, most of the energy would go into the upper atmosphere.
Let's say a 100MT bomb detonated on the sea floor. Say, 60 miles offshore from Los Angeles, where Google Earth shows places up to 5,000 feet deep. The tamping effect of the water above it would let a lot of the shock-wave energy go into the shelf.
What would be the effect of that on the San Andreas fault?
The fault probably would not 'notice' it much at that range. That's a lot of earth and rock to move.