You mentioned viewing pictures on the back of the camera and comparing the contrast: I don't really think you can make a comparison with that, as the LCD screen on the camera is not exactly calibrated. Did you always view the histograms in LR? Because of course the D300s camera-back histogram is based on the jpeg not the raw, so is not reliable for judging raw.
"My light meter told me, that in several of my shots, the background was almost 6 stops or more underexposed, which to my knowledge translates to pure black, where the sensor is picking up no light and hence no detail." The dynamic range of the sensor is more than 6 stops, especially with raw. The histogram on the camera back will be limited by the jpeg (8 bits, so a maximum of 8 stops) but according to the dpreview tests the D300s sensor can produce more than 10 stops dynamic range.
As you say, a blank image will show values of 0,0,0 with the blacks slider at 5, but the values increase a bit if you slide it to 0. No idea why, but remember that the rendering of raw values to processed values is quite complex, and it may be that black (zero) values are not always clamped at zero through all transformations.
