Yes, this is true -- Parshall and Tully mention it in Shattered Sword, which is currently probably the most reliable book on the Japanese experience at Midway. I don't have a physical copy with me for page numbers, but it's in the chapter called "The Iron Fist," in discussing the American dive-bomber attack. I won't swear to it, but I believe this is also brought up in Lundstrom's The First Team and Walter Lord's Incredible Victory.

There are a couple of spots this is mentioned in Shattered Sword -- for example, when Dick Best and his two element-mates attacked Akagi, Best aimed at what he thought was the island but was actually a protruding stack (boiler uptake) on the starboard side; one of his wingmen specifically aimed at the hinomaru. In the attack on Hiryu, the after-action report showed that all four of the 1,000 pound bombs that hit the carrier landed on the forward third of the flight deck.