Ah the Hand. They are Marvel's mysterious equivalent of the Yakuza. The Hand rule the criminal underworld of Japan with an iron fist, using ninjas to enforce their whims. These silent and deadly assassins make the Hand particularly terrifying since they are able to strike quickly and silently to eliminate their foes.
But how effective are ninjas once superheroes are thrown into the mix? The Hand have frequently found themselves in conflict with the likes of Daredevil, Wolverine, Electra, and other costumed heroes (including the New Avengers and the X-Men). In all of those cases, the heroes have come out on top, resoundingly trouncing the Hand and their well-trained enforcers. Granted this is usually the outcome whenever a criminal organization goes up against a hero or heroes, but the amount of energy required to train hand ninjas makes these losses even more devastating.
Let's break it down. In order for a single Hand ninja to be an effective enforcer, they require a certain baseline level of skill. To be effective, the average hand ninja needs to be able to at least take out one average street thug with a gun. But the training required for a ninja (who fights primarily with short range melee and thrown weapons) is obviously greater than the training required for the average street thug. In order to be a threat, a Hand ninja needs to learn the use of multiple weapons and martial arts styles quickly and effectively. The ninja also needs training in stealth. By cultivating these skills, a well-trained Hand ninja will be able to negate the inherent advantage provided by using a firearm, allowing the Hand ninja to dispatch his/her enemies with style and efficiency. But this can only be achieved by having a ninja train extensively for many months with several masters of respective styles and skills (swords, shuriken, stealth, etc.).
It also seems likely that the Hand will need to recruit individuals into their service who are outstanding physical specimens. Proper ninjas need a baseline amount of speed, strength, and dexterity that not every human being possesses. As a result, the Hand would need to screen and recruit applicants prior to their ninja training. And in some cases, the Hand ritually murder their trained ninjas and resurrect them to give them superhuman strength and endurance. This ceremony takes at least a day and requires the efforts of a dozen of the Hand's gifted sorcerers. All in all, this is a lot of time and energy invested into a single Hand ninja.
And then Wolverine kills several hundred of these ninjas in a single day. The investment hardly seems worth the return.
To produce a single ninja requires at least several months and the continuous effort of multiple ninja trainers. Hundreds of man-hours are expended. And Wolverine merely needs to flick his wrist to negate all of that effort.
In a world where heroes can wade through your well-trained sycophants, it certainly seems more economical to hire random thugs with some marksmanship training and provide them with automatic weapons than to imbue hundreds of ninjas with mystical powers. Sure, undead ninjas are cooler but if they're just going to be torn apart anyway why not save yourself the time and effort of training your cannon-fodder?