I solved the problem of my rear spring covers rattling by the simple expedient of chucking them away. I was worried at first that I would get water, mud, and other crud coming into the cockpit, but it just doesn't seem to happen. Mine were secured with basic woodscrews, bu then my car was built in 1986, when MMC quality standards were in the Stone Age compared to what they are now.
I have to say though that I think they are unlikely to cause a clonk, I would be checking rear spring bolts and linkages, battery security, U bolts, and rear wheel tightness.