The hard top of my 300SL is never on the car. With the top down my experience driving over rough pavement and small bumps is similar to yours. Cowl shake is quite noticeable. This is in marked contrast to my experience driving W107 and W113 SLs.

I suspect there is nothing wrong with your car or mine. I looked at a recent issue of the English magazine Car and the brief comments on the R129 SL500: effusive praise, but they were critical of excessive cowl shake.