There are a lot of things more into it. Actually, it was a special attack created by Minato to mark a different location in the battle area by throwing a lot of kunai's to take full advantage of Flying Thunder God Technique in the battlefield. The Flying Thunder God Technique is a space–time ninjutsu created by Tobirama Senju.
Kunai were historical tools/weapons used by ninja in Japan, though their uses have been expanded/fictionalized in Naruto. I think in Naruto, they function as versatile long-distance and close-range weapons that can be used even if someone is low on chakra or trying not to attract attention. One thing to also keep in mind is that Naruto and Sasuke (and the like) are the kind of absurd extremes ...
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The Trap Card Kunai with Chain can add 500 additional ATK to a monster. If he had summoned Red-Eyes and allowed Yugi to attack with Gaia, he could have activated Kunai with Chain and defeated Gaia without his original needlessly complex strategy, saving several cards that could be useful later.
yu gi oh - Why didn't Jounouchi just use Kunai with Chain? - Anime ...
A kunai can never penetrate Gaara's shield or any other strong defences, but Rasengan and Chidori can. Oodama Rasengan and Rasenshiriken are on even greater levels because their damages are astronomical. In the fight with Kakuzu, before Naruto came, it was incredibly hard for the others to stall out Kakuzu, let alone finish him.