Yes, it's yet another 3DS thread.

As anyone who has seen a 3D movie, there isn't just pop out, but pop in. That is, we see depth into the screen much more realistically than we would with just a 2D plane. In gaming I see this as almsot essential, showing what is well in front of your character as happening "behind" the screen. With movies, this isn't a problem since the screen is against a wall, so our brain can think of it as a window. With the 3DS however, our hands are behind the screen, so we will be seeing action happening where our hands, as well as the rest of the room also is. Will their be a strange cognitive dissonance caused by this?

Even more wiers is my other thought related to clamshell. How is screen pop out going to work at different relative angles of the two screens. If the bottom screen is having things pop above it, and the top screen is having things pop in front of it, what happens when images collide? How does the game properly distance the 3D pop out from the two screens? Does this mean that only one screen is going to have 3D to prevent something like this? Will their be prescribed angles of screens?

A press demonstration of the 3DS can't some soon enough so that these questions can be answered (especially the second one).

It probably won't pop up many inches above the screen, so the only way to colide the images is by closing the handheld completely.

As for your first point, it's the same as viewing 3D on a laptop. Sure it seems that it is something happening back there, but it doesn't cause any confusion at all, at least for me...