One problem with the "depth charge" analogy is that depth charges rely on a property of liquid water not shared by a gaseous atmosphere: water cannot be compressed. They use this to greatly amplify their range of effect.
Second problem is modern ground-based skyscrapers are already engineered to withstand shocks, and buildings on floating platforms in a thick atmosphere would have to be be engineered against even stronger shocks by their very nature.
Shock Wave In Water
Unlike a gaseous atmosphere, the density of water does not change with depth or pressure. It's always going to be about 1000 kg/m3. It's incompressable. The increased pressure with depth comes from your vessel having to hold up an increasingly large column of water above it.
When a depth charge goes off underwater, the volume of the formerly solid bomb is rapidly turned into very high pressure gas. This expands against the surrounding pressure of the water. Since water is incompressible, the expanding gas shoves it out of the way in an expanding shock wave until the pressure of the gas equals the pressure of the water, then water rushes back in creating another shock wave. This goes on until the pressure equalizes, or the bubble reaches the surface.
The first shock is damaging, but the following cycle of inward and outward shocks can break a submarine's back as it is first bent one way, then the other.
The effect is devastating, but because the pressure underwater is so high, and water is so dense compared to air, the range is rather short. 100 kg of TNT needs to be within 3 to 10 meters to disable a submarine.
Shock Wave In Air
A shock wave in air is different. Air can be compressed. Again, the solid bomb becomes a ball of gas expanding at supersonic speed pushing against the surrounding air. The air cannot get out of the way fast enough, so it compresses into a pressure wave in a sphere around the explosion. The explosion is like a plow going through the earth building up a bigger and bigger pile of dirt in front of it.
That pile of air, the pressure wave, smacks into things. Since it's so much less dense than water the wave can travel further, but it has a much diminished effect from a depth charge.
There's also no cyclical rebound effect to cause the flexing that is so damaging to ships. Instead, as the explosion expands there will be a brief low pressure zone in the center and you'll get a second, much weaker, pressure wave going back towards the center of the explosion.
You can see this in old atomic bomb test footage. First the target starts to smolder, that's the light and heat hitting it first. Then the shock wave hits and typically blows everything apart, followed by a second rush a air backwards.
Shock Waves Vs Buildings
If your buildings are engineered to withstand the rigors of flying through a turbulent atmosphere, they're already built to withstand shock waves.
Your buildings have to withstand the shifting of their bases as they float and maneuver through the atmosphere. This would be very similar to modern earthquake engineering designed so the building will dampen the effect of the ground shifting under it. The shock of a bomb going off well under the city would have a similar effect and the building would be designed to weather it.
Tall buildings also have to be engineered to withstand the wind pushing against their sides, the lateral wind load. A flat slab skyscraper is basically a big sail. Too rigid and it will snap. Too flexible, and it can oscillate; if the wind gusts just right, it will tear itself apart as what happened in the Tacoma Narrows Bridge.
Modern skyscrapers are engineered to be flexible, but also have buffers to prevent oscillation. They're also engineered to be aerodynamic to cut through the wind.
All these engineering necessities of a ground-based skyscraper are even more necessary for a skyscraper on a moving platform in a thick atmosphere. They'd be greatly buffed up and even more able to withstand the shock wave from bombs bursting nearby.
