To me, "skyscrapers in space" feels like an attempt to capture the majesty of World War I and II battleships. Which is to say, not much better justified than the aerodynamic spaceship. I don't see why a hard-SF spaceship really needs to be big when it would still be quite fragile (given the energy of an orbital-velocity collision).

That is, unless you design your future weapons and FTL drive principles so they really do reward "bigger is better" (I'm on to you, David Weber.)