My understanding is that the in-camera distortion control doesn't effect raw images (other than to put the setting in the NEF metadata). I think the camera applies distortion control (when enabled) only on jpegs - including the jpeg embedded in a raw file. So it should have no effect on Lightroom.
However, Thom Hogan yesterday said auto distortion control does
effect raw - see http://www.dslrbodies.com/cameras/camera-faq/which-camera-settings-apply.html
. However, in his D800 manual he says that raw files are not affected (p451).
I've checked again today: took 2 raw photos of a test target (on a tripod), one with auto distortion control on, the other off. In Lightroom (and ACR) neither have any distortion control applied. If I open the images in Nikon Capture NX2 then it applies distortion control if you set it on in the camera, not otherwise.