Yes, it does give a guide number change. Using a 3 stop ND filter will quarter your GN. It cuts both ambient light AND flash light going into the lens. It affects both in the same manner, so you can slap a 3 stop filter on and open your lens up 3 stops, in the real world. If you needed a 1/1000 speed to get your ambient balance correct at your chosen aperture, you could put a 3 stop ND filter on and get the same balance at 1/125.
If you're running around doing fill flash with 3 stop ND on and 400 speed film, you'd have to calculate flash exposure, as well as ambient exposure, like you were shooting 100 speed film. So, yes, it does effect flash GN.
Originally Posted by MattKing
If the ND filter is on the lens, it will decrease the brightness of both the sunlight and the flash equally - at the film plane.
But if you have enough flash power to, for example, achieve appropriate fill at 1/500 at f/8 (assuming EI of 125 and a leaf shutter) then a 3 stop ND filter will allow for the same result from 1/500 at f/2.8.