Yeah. A katana is designed for the quick kill. In fact, there is an entire stance in kenjutsu devoted to the art of striking an opponent as the sword is drawn (popularised by Rurouni Kenshin) called Battojutsu or Iaijatsu. The idea behind it is to reduce air resistance by drawing from the sheath creating a vacuum, allowing the blade to move at 2-3 times normal speed.

The Masamune would be too slow to kill anything outside of the video game world.

Quote Originally Posted by Gilgamesh of Legends
Ninja's didnt use special swords, they were regular katanas, sorry to burst your bubble
I don't know much about ninja's but I'm sure that their weapon of choice would have varied with personal preference. It's not as if there was a law stating that a ninja HAD to use a katana. In fact, the ninja with kunai is probably more stereotypically recognisable than one with katana.

EDIT: New source states that ninja favour shorter blades called Ninja-to, which are longer than a Wakizashi but shorter than a Kodachi. The only reason why ninja are more recognisable with kunai is because Naruto popularised it.