The electric motors (stepper motors) that operate the climate control vent and temperature doors can make clicking noises. If you are experiencing any problems with the airflow or temperature of the climate system, I would definitely suspect one of the motors is failing.
There is even a technical service bulletin (TSB) from Mercedes about this issue, here is a summary:
"If you receive customer reports of a ticking noise coming from the area of the instrument panel, incorrect air distribution or whistling sounds from the vents, the cause could be malfunctioning stepper motors or damaged lever arms"
A good Mercedes shop should check to see if this is indeed the noise, and have this bulletin and the ability to test and repair this issue. Here is the bulletin # P-B-83.00/78a