I had the same problem as well, In my case it is not a Shotcut problem but a camera problem (Canon SX280). But this is how I solved it.
Of every video cut a tiny piece off the first bit of the video, not much, just let us say 0.2 to 0.5 seconds or something like that. if needed you can use the audio fade in for 0.02 Seconds. No more clicking noises after that.