Possibly because sensors can detect and lock a reticule on any ship at that point, and you'd want to be able to see your wingmen so you don't ram or shoot them, especially a big black-painted Broadsword.There's certainly a precedence in the Wing Commander universe -- there's fighters with "ground camo" and "stealth camo" in the novels... and then there must be a reason things like WC2's Broadswords are painted green.
I don't have Photoshop, could someone make a Claw Marks-style line drawing for the Pirate fighter?