Yugioh ninja monsters have been out for quite a while. In fact, one of the first ninja monsters, Strike Ninja, was considered so lethal that it had to be banned. One of the first Yugioh cards ever made was a ninja, Armed Ninja (he was a nuisance to duel against ‘back in the day’). A few other ninja monsters came out, but ninjas were not very popular until the release of Order of Chaos. The booster pack has released many new types of ninja monsters and has cemented ninjas as one of the more popular archetypes in Yugioh.
Just because Ninjas aren’t well-known doesn’t mean they aren’t bad. With two powerful ninja monsters being released in Order of Chaos, Number 12: Crimson Shadow and Blade Armor Ninja, they are quite a force. Usually, ninja decks revolve around pestering opponent’s with various Ninjutsu spells/traps. A powerful Ninjutsu card is Armor Ninjutsu Art of Rust Mist, which halves the attack of any monster special summoned on your foe’s side of the field (as long as you control a ninja). This trap greatly weakens synchro and xyz support in your foe’s deck and is a staple in any Ninja deck.
In terms of monsters, Ninja decks usually relied on Dark Simorgh, since a majority of Ninja monsters was compiled of wind and dark monsters. Thus Dark Simorgh can be easily played in a Ninja deck and is a great monster: not only does it have 2700 attack points, but it also prohibits your opponent’s from setting cards. With the release of Order of Chaos however, Number 12: Crimson Shadow Armor Ninja has become the ace of the ninjas and with good reasoning. Not only does CSAN have 2400 attack points, but by discarding one material monster (two in total, level five), ninja monsters cannot be destroyed by battle or by card effects. Pretty awesome effect.
Ninjas are a very fun archetype to play with. They may not be the best archetype, but they are pretty good and can be tournament-level with proper construction. On dueling network, I have been using ninjas a lot and are 11-7 with them, which is a pretty good record.