Your question isn't exactly a duplicate.

With Adobe Camera Raw (ACR), you are creating and saving your changes to a sidecar XML file with an XMP extension. With ViewNX or Capture NX (Nikon's raw processing software) you are making changes directly to the NEF file.

As with ACR, you are not changing the raw image data†, just the image-processing instructions. But those changes will overwrite the values that were stored by the camera when the NEF file was created, so things like a custom preset white balance or a selected picture control will be altered from the original. You can always work your way back to the original settings (the original raw sensel data are still there), but it's not as simple as deleting an XMP file when you realize you've made some horrible mistakes along the way.

† I can't be absolutely certain, but I think the dust-off picture data, when used in CaptureNX, is actually applied to the raw image data. That would certainly make sense from an economy point of view; the alternative is to store an entire separate set of sensel data values in the same file.