Clocks are synced for all players in the same server. With non-zero pings the server, indeed, can only send old position data, or better to say, it sends current positions, but when clients receive them, the data is a bit old. So, a special netFM extrapolates the positions of planes, effectively predicting where a craft should be, based on previous positions. When a craft flights straight the predicted position practically matches the real one. In turns - the sharper the turn, the bigger is the error between the predicted and 'real' position - and since it depends on ping, it is slightly different for all players.
What we are changing/tuning currently, is this extrapolation (prediction) algorithm, to make it more robust and, err, predictable (no pun intended) in the modern network conditions.
So, the missile accuracy should actually improve a bit, not to get worse. If it has really become worse, something is not right in the missile code, not in netFM. We'll take a look.