The problem I see here is not actually whether present Nikons do this or not, but the trend of the camera vendors. If they start to play unfair pre-processing their RAW data to obtain cleaner RAW files, it will become difficult to make fair comparisions since detail and sharpness tests should be done in addition to noise measures. ).
But where does one draw the line?
Example 1: Bad pixels (i.e., pixels that are always effectively clipped to white or black). They contribute to standard noise measurements unless you use robust statistics designed to ignore them. Is it ok for a camera to fix bad pixels before writing out the raw file?
Example 2: CFA sensors often have 2 green pixels. Sometimes the two green pixel types differ significantly in response. Is it ok for a camera to balance the greens internally before writing out the raw file? (Keep in mind that green-balancing is effectively a form of noise reduction.)
Example 3: Tiling issues. Large sensors are sometimes composed of multiple pieces which have differing responses. Is it ok for a camera to "balance" the signals across the components before writing out the raw file? (Essentially performing an in-camera calibration.)
Example 4: Lens corrections, such as distortion. Is it ok for a camera to apply geometric distortion correction automatically before writing out the raw file?
(I submit these as real-world examples of things that camera makers either already do, or will be doing.)