Are you sure it actually has an ND filter? In the code submitted for svn, HAS_ND_FILTER was undefined. Cameras that have an adjustable aperture and an ND filter (like the G series) generally give you ND control in the Canon firmware. The specs and manual don't mention this, so I'd be quite surprised if it had one. The option could have appeared in the beta build menu even if the hardware wasn't there, but it wouldn't do anything. The ND filter should change the exposure by 3 stops, so it would be very obvious if it was working.
Yes, turning it on definitely reduced exposure.
Case: photographing very bright reflections on water. Using the max 1/3200s exposure and F/8.0 there are still blown-out highlights. Turning on ND filter gives substantially darker image, without blown highlights (or with much less). I can definitely say that it makes a significant difference. This is very handy for HDR photography.
I read somewhere that the camera had an undocumented ND filter, and mine certainly does seem to. Could the HAS_ND_FILTER define have been accidentally removed when going from the beta to the release version? Beta5 definitely has the ND filter option and it definitely does something on my camera.
I've switched back to Beta5 for now. (BTW, the ND filter option has a bug in Beta5 - when ND is in, half-pressing the shutter button and then releasing it again crashes the camera. All is fine so long as you actually take a picture.)
EDIT: BTW, activating the ND filter does not affect the preview display until the shutter button is half-pressed, so people testing might think the option has no effect unless they actually take a photo.