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I know that Madgwick provide two type of sensfusion algorithms, one for IMU 6-DOF and a version with Magnetometer. I've checked CF code and didn't find any implementation of magnetometer, just as log. There is particular reason for this like motors interferences, heavy computationally code or else?

Do you think it's possible to avoid Gyro drift on Z axis using a HPF?(loosing probably some precision)

One of the main reason is that we mainly use the Crazyflie indoor and the magnetometer will pick-up things like computer and other metalic mass inside. But the magnetometer could be used outdoor with the gps deck or indoor with other controlled magnet.