A festering ventilation system is a real health risk, and if yours smells dank and musty when switched on, it’s something well worth combatting. It’s possible that at some point in the car’s history, dirty flood water, sewage or countryside effluent has found its way down the external vents and into the system. This means that a thick carpet of mould and bacteria may be coating not only the heater, but also the ducting and fan blades.
Unfortunately, there’s probably no alternative to removing and cleaning all the parts with soap or a household antibacterial cleaner. Strip down for your particular model should be detailed in your manual, so carefully remove all the heater components including the matrix for thorough cleaning. It’ll be impossible to clean the individual fins of the heater matrix, so soak it in a solution of disinfectant overnight and use a water jet for final cleaning. We’d suspect this would be self-sterilising, though, as it runs at 80°C when in use.