Originally Posted by Mal
It was more concerned with covert skills, which almost never involved sneaking around at night in a black suit. First, because a dark blue would have been used since black is unnatural; second, because most espionage/infiltration was done just like it is today (ie. getting someone on the inside or just threatening/paying off someone already there).
Not to mention the "black suit" is a Hollywood construct. That idea was taken from stage hands in kabuki plays that would dress in black to better blend in the shadows when they had to move props during a scene. Ninja were more likely to wear farmer's clothing or monk robes than the black suit.