Note: This is a repost from my question that has yet to be answered.
If I understand the events of Midway correctly. The Americans set a trap for the Japanese by asking those stationed at Midway to sent a faux request for a fresh water tanker. When the Japanese reported this, the Americans knew for certain that the Japanese were targeting Midway.
"A.F is short on water"?
Why would the Japanese have transmitted refer to Midway using the US designated A.F? Why wouldn't they have used their native language making it harder for the Americans to know what they were referring to?
"AF" is ultimately derived from the way JN-25 is structured; as others have mentioned, it's a 5-number code that can common words/phrases in japanese, but also can encode numbers and letters of the Latin Alphabet - needed for transcribing names of American ships or locations that aren't specifically mentioned elsewhere in the codebooks, but also, likely as mentioned by others, due to the difficulty of covering all Japanese alphabet combinations in the codebooks.
The Japanese did have a habit of using latin letters for locations- some previous operational successses had been the decoding of R for Rabaul in 1942, and RZP as a desgination for Port Moresby. And part of the reasoning behind AF being Midway was that Rochefort knew that "A" designations tended to be American held Islands in the Central Pacific (mostly Hawaiian Islands)
(https://www.afio.com/publications/OLESON_WIMAD_Breaking_of_JN-25_from_AFIO_Intelligencer_Vol26_No2_WinterSpring_2021.pdf)
(https://stationhypo.com/2016/05/27/path-to-midway-tactical-loss-strategic-victory/)
Other examples include what the Allies Called Operation U-Go (The Japanese advance on Imphal and Kohima in 1944), the Japanese called Operation C. Operation Ichi-Go (the advance on Allied controlled Airfields in Southeastern China) literally translates to Operation 1.