3D Model would be useful for several reasons. One is you could know the exact height of the board and can integrate that into your project's 3D model. I am planning on building a quadcopter soon and I have the 3D Model of the frame almost ready except I don't have the Arduino board mounted.
But you're right, a 2D CAD file would be more than sufficient for most people. I just wanted to bring this to attention since it is not that hard to come up with a dwg file and post it on the official website for people to download along with the EAGLE files.
s there a standard practice for this sort of thing that enables the 3D model to say "here are standardized components like the shield connectors, and here is a bunch of stuff whose details are unspecified, but will have height less than X" ?
^ I don't understand what you're trying to say here...can you please elaborate?