I'll try to keep this simple without going into too much about anatomy and physiology.
Lets say I give you pain killers and push you over. Yes you're not feeling it right now. But it doesn't mean you're not getting the shock or the muscle tears from it.
If anyone's got a better analogy please share. Thats the best I got
IMO you can hit through hard hit balls better with a flexible racquet where as a stiff racquet causes your joints and arm to do the stretching and flexing to the load.
Man I love my Boris Becker DC London 93... :P