Film makers have a lot to answer to. Ninjutsu is a martial art, in fact, fighting was a last resort - ninjas were skilled in espionage and defeating foes using intelligence, while swinging a sword was deemed a lower art.
They couldn't vanish as they do in the movies but, being skilled with explosives, they could make smoke bombs to momentarily misdirect the gaze, then escape.
Yes! they did wear black. Ninja clothing was made to be light and hard to see in the dark but, jet-black would cause the form to stand out in moonlight, so a dark navy blue dye was usually used.
I'm sure the ninjas will not be forgotten, but the once-feared secret assassins are now remembered chiefly through fictional characters in cartoons, movies and computer games, or as a tourist attractions. ;-)