I think it is very likely that the buoyancy of the rocket is taken into account. First, let us see what savings it gives in terms of mass:
What is the density of a rocket? That is actually quite difficult to find, but considering a kerosene/LOX rocket like Soyuz, it is mostly propellant anyway. Kerosene has a density a bit less than 1 kg/L, and LOX a little bit more. As the rest of the rocket is metal, that should average out a little over 1 kg/L. Continuing the rough approximation, that means that the Soyuz rocket displaces around 350 kg of air. Is that much? For a comparable number, the Space Shuttle External Tank was painted with reflective paint on the first two flights. Then they decided that it could actually be skipped, "saving approximately 272 kg"
Rocket science is all about small margins, and that means there is a fight for every kilogram. As the effect of buoyancy is within the magnitude of other things considered, it is almost for sure taken into account.