White capping, as in 8-10 m/s wind in sheltered areas, seems to pose no problem at all. Peak storms (all the way to hurricanes), the same thing - we have seen great AST data all the way up to 8-9 m significant wave height. The build-up of a large storm with breaking waves that entrain large clouds of bubbles - clear increase in the number AST drop outs. Not everywhere and everytime but in some places and some times. Acoustically this makes sense since scattering from bubble cloud can give very high signal returns.
The backup solution is to measure velocity below the surface or pressure. Since the problem only seems to occur when there are large events (Hs > 3-4 m) the orbital velocities are strong and the pressure fluctuations significant so the backup solutions works quite well.