Is this a bug or simply conservative estimation on Nikon's part? As I understand it, the RAW compression is loss-less. So the amount of compression possible differs from image to image. In the worst-case, the image cannot be compressed (or rather the "compressed" image is larger than the uncompressed version).
So maybe Nikon's just being conservative in giving you a shots-remaining count that will not be too high. It's much better that you have more shots than you think, than for the camera to tell you that you have more shots available than there actually are. Since the shots remaining counter is updated after every image, on the recalculation it should take into account the size of the compressed RAW file that was just written. So you should see the shots remaining counter decrease by less than 1 for every shot that you take (since it's quantized, for some shots you'll see it drop by one, for others it will remain the same).
This is just speculation on my part, since I'm still sitting on the D100/S2 fence clutching my wallet.