Yes. If you want to think of the shape as a square, you can equate its area A to a more efficient shape for bending (or buckling) calculations. But for your biggest question, a truss member just uses area A regardless of shape. Shape isn't specified (except in a buckling analysis). So it doesn't assume a square. But if you're applying any transverse load to your member, then it's a beam member, not a truss member. Simply-supported beams (or pin-connected beams, neglecting axial shortening) just need any reasonable I value, regardless of shape, to get end reactions and internal forces. But to get beam stresses, the shape must be specified because you must use the correct moment of inertia I and extreme fiber distances (stress recovery points) for the stress calculations. Hope this helps.