Yes. The autofocus noise is usually coming from the lens motor and can be picked up easily by the camera’s built-in mic. Some lenses are quieter than others, but if you want to really reduce or eliminate the recorded focus noise, the best solution is to use an external microphone placed away from the camera and lens.

A shotgun mic can help because it is directional and can be aimed toward your subject instead of the camera. More importantly, increasing the distance between the mic and the lens reduces how much focus noise gets recorded. A mic mounted directly on the camera may still pick up some mechanical noise and vibration, while a detached mic on a cable or wireless setup will work better.

In short: quieter lenses may help a little, but an off-camera external mic is the most effective fix.