On an actual 3ds, in first person, you get stereoscopic 3D.
After Naked Snake loses his eye, you no longer get stereoscopic 3D in first person, because Snake himself no longer has 2 eyes with which to see in 3D and perceive depth like the 3DS screen.
Great port. Genuinely amazing port quality for that alone. Totally unnecessary but lore accurate addition that immerses the player by surprise.