The problem with making a "real" ninja in any game setting is setting the definition. In the Legend of the Five Rings (AEG editions), ninja is a real class option that is limited to one clan. They fit the stereotypical ninja of Japanese lore, but their mystical powers are much more misdirection than actual magic. There are also the true ninja not aligned to any clan, which have magical powers granted by the Shadow, a mythical being that wants to unmake existence. Both are ninja, but they fit different definitions of the term.
Another problem is the fanboy issue. Look at how many people were upset that the katana was "only a longsword," rather than the uber weapon of destruction they feel it should be. Making a ninja in D&D would suffer the exact same thing, where they're supposed to be able to do everything, rather than being specialists (spy, assassin, saboteur, martial arts expert, etc.). Rogue can cover the first three specialists with different sub-classes, while shadow monk easily covers the last.