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Extruding a feature point by a constant or expression, and changing the view setting from perspective to orthographic view make the data disappear from view.
ArcScene uses OpenGL as its graphic API. OpenGL cannot display lines when viewed head on from end to end. When a point is extruded it becomes a line. When a viewer is placed in orthographic mode, you view the line head on. While you expect to see a point drawn in 2D you see nothing.
Buffer the points and extrude the resulting buffer polygons.