Test NEF files are a available at this link.
Using this code it is apparent that the image data is not clipped by Mathematica.
img = Import[a.NEF];
ImageHistogram[img, 1000, All, Appearance -> "Transparent",
Method -> #, ImageSize -> Large,
FrameTicks -> True] & /@ {"IncludeOutOfRange", "ExcludeOutOfRange"}
