The book "Shattered Sword" is probably the best, most highly-detailed, and fact-checked book ever written about Midway. It includes data on the positioning and appearance (yes, there were differences) of the Hinomarus on the four lost CVs. Serious Pacific War wonks generally regard it as definitive. At the same time, there is a message board called "J-Aircraft.com" which has an absolutely wonderful IJN warships Q&A, and the board is extremely active amongst both Western and Japanese Naval history and warship buffs. It is a deep trove of data down to the level of minutiae - well-worth registering (free). Finally, while it's not a CV, the Submarine tenders Chitose and Chiyoda both had large amidships, flight-deck like structures which had VERY prominent Hinomarus painted on them... They were carried as late as the Solomons Campaign and were quite large... smaller, of course, than one the size of that carried by Akagi or Kaga, but considerably bigger than ones carried on some IJN DD "A" turrets early in the war, or those carried on the main-battery turrets of a couple of IJN BBs. I will also note that the ones on the DDs and BBs were hinomarus pointed over a large, square white area and mimicked the Japanese national flag. Those on Chitose/Chiyoda were painted straight on the deck with no white square, but with a white surround (i.e. as on an aircraft). I hope this helps. IIRC Kevin Stewart is also an IJN fan, so maybe he'll see this string and also chime in.
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In addition to the Hiryu, Soryu, Kaga, and Akagi it seems that possibly 4 or 5 other IJN carriers may have had the Hinomaru painted on their flight deck. 3 or 4 of the carriers were also part of Operation MI (Midway Invasion). The model references I have show the Hosho, Zuiho, Ryujo, and maybe the Junyo might have had the Hinomaru painted on the flight deck. I only implicate the Junyo because I have a model reference showing Junyo's sister ship Hiyo wearing one on her flight deck in July, 1942. Hiyo was comissioned too late for the Midway Operation. Attached are some of the pics and drawings I have found.
IJN Hosho
IJN Zuiho
IJN Hiyo
IJN Ryujo
Does anyone else have any better pics or references that would verify the existence of the Hinomaru on these or other IJN aircraft carriers?