I think we could define the horizon as the apparent line that divides the earth and the sky. That being said you are right that the horizon isn't necessarily perpendicular to gravity. Therefore, we can pretty quickly say that gravity based horizon information won't be a good solution, except perhaps for a seascape, to show you the actual horizon.
Moreover, if you're out in the natural world, items such as trees aren't at all necessarily vertical, as you mentioned, but in the human-made world, generally the orientation of columns, but not necessarily the edges of the columns (Parthenon), and most exterior walls of most buildings are vertical and run parallel to gravity. In fact most building construction these days is vertically "plumbed" via gravity, or laser sited via gravity. From there they get the horizontal the building should be built to. So, a gravity based horizon should work nicely for cityscapes.
Yes it would be a nice feature if Nikon would include horizon information in the exif data, for cityscapes, but to be honest by using a vertical or horizontal guide in Photoshop, I've really not had a difficult time "straightening" my photos as necessary.
As to the virtual horizon in the D3. It doesn't have to be behind menus, if you think it's important to you to have at your fingertips. For example, your could assign it to your FUNC. Button. (See pages 331-333 in your manual.)
As to shooting sports, it takes conscience practice, but you can get darn good panning quickly on a monopod, and keep your camera horizontal. If it's off, use visual guides to help you rotate the image to correct the problem. Lay the guide on something you feel is either horizontal or vertical.