I won't pretend to know how the D16's aerodynamics work, but the smaller the surface area the less the aerodynamic resistance. A lot of other things come in to play though, namely shape.
We gotta think of the D16's shape and size as a function of compromises between top speed and cornering "flickability". Long streamlined fairings are more conducive to top speeds, but shorter fairings assist in making side to side transitions easier.
As far as the switch from 990cc to 800cc, I would speculate that the emphasis on cornering speed in the 800cc era over top speed in the 990cc era means the 800cc bikes need shorter, more compact fairings... again I'm not an aerodynamicist.
The RR is based on the 990cc machine btw, but its bodywork is actually quite different from that of the genuine race machine.