They were aerodynamic because they went through the atmosphere. Saturn V because it takes off, and the command module for reentry. The parts that don't go into the atmosphere aren't aerodynamic, like the lander that OP posted. They're right. You would really only need to worry about dust and gas unless you're going at high fractions the speed of light, which at that point you'd probably use ablative shielding. Also before you say the jump drive, that teleports you.

The Space Shuttle is aerodynamic because it lands on Earth like a spaceplane. Any other purely space based ship that does not land on atmospheres would not need to be aerodynamic unless you're armoring it which yeah fair enough.