The control stick module itself is responsible for the sound. This noise is meant to happen when the clicker switch on the flexible PCB is pressed down. If your L3 input still works and the Joy-Con is not exhibiting unusual behavior or resistance when moving the stick, I wouldn't worry about this. If functional issues come about as a result of this matter, the most convenient method of resolution is changing your control stick module. For the left Joy-Con, you can do this by following [guide|113182|this|new_window=true] guide, which is also available below for your reference.
In the future, be wary of using excessive force when pressing the L3 and R3 buttons, which is a potential cause of failure. I hope your problem is resolved without too much trouble.