it seems they didnt wear completely black gear and that red is not at all 'bright' in darkness
As I understand it, the black ninja comes from traditional plays. In the plays the ninjas are invisible assassins and so wear all black to disappear against the black background of the stage.
The real life ninjas were infiltrators. They'd dress up to fit into where they were going, do what they had to do, then leave.
More Mission Impossible and not so much League of Assassins.