The issue of Himiko not being mentioned in Japanese sources has less to do with purposeful omission and more with issues of how the Japanese began to keep records and the introduction of Buddhism to country in around the 6th century.

The kind of wide spread literacy and record keeping that is present in Korea and China at the time are not present in Japan. Chinese sources (The Chronicle of Wei) talk about interaction with the Kingdom of Wa (a somewhat derogatory term meaning "Kingdom of Dwarves"), which ranges anywhere from around the 200 BCE to 100 CE depending how one interprets the Chinese dating system. Japan of this time had been in contact with the mainland for hundreds of years, and imported many experts to assist with rice growing and irrigation techniques. Also present were scribes, but who almost exclusively wrote in Chinese. Until about the 6th century CE, the Japanese did not generally use Chinese characters for the purpose of government or personal writing. It's not until widespread adoption of Buddhism and the adoption of the Taika reforms that extensive record keeping, especially histories and government business, begins to occur with any regularity or in an official manner. So while there existed, and may still exist, documents which describe Himiko from a contemporary Japanese perspective, these would not be any sort of official history or go beyond a personal diary or letter.

As part of creating a legitimacy for his new government under the Taika reforms, and to further mimic a Tang Chinese style of government, Prince Shotoku commissioned the writing of the Nihon Shoki as a dynastic history of his Yamato family line. This history is the primary place in which the family connection between the Emperor and the Sun Goddess is codified, the various mythos of the creation of the Kami and the islands of Japan are collected, and is essentially the earliest document available that describes any time prior to the 6th century from a Japanese perspective. The document is also concerned with the succession of the Emperor from Amaterasu, and places the first "grandson" of Amaterasu as Emperor Jimmu. Jimmu, or at least the man we think was Jimmu, probably lived around 350 CE, around 200 years after Himiko would have lived. To further complicate things, the Nihon Shoki was not translated from Tang dynasty Chinese into Japanese until the 18th century by a man named Norinaga. His translation of the Nihon Shoki is arguably the ultimate work on the subject. Yet, it is still a translation, and possibly contains errors or interpretations of the translator.

This is to say, after all this ramble, that there is no reliable source for early Japanese history. Documents like the Chronicles of Wei are the only insight aside from archeological evidence at early Japanese culture and life. The Nihon Shoki is first and foremost a dynastic history, and is designed to aggrandize the Yamato. The most important way this is done is through Amaterasu and the connection the Kami. This connection to the Sun Goddess is congruent with the centralization of authority around the High Priestess mentioned in the chronicles and the evolution of Japan's political structure from the Yayoi period into the early Heian.

Within the social structure of early Japan, clan was the most important distinction between various groups. These clans tended to be collected around a professional class or a social function, and split between Uji clans (mostly aristocratic, military, and priestly families) and Be (professional classes, such as blacksmiths, potters, weavers etc.) Most Be were not as formally organized as Uji. At the head of each clan would be an Uji-gami, or a family diety/spirit (Uji - Clan, Gami = Kami) whose worship would be directed by the head of the family. This is where Himiko as a "Sun Princess" is important. If Himiko's family was large and powerful, and worshiped the embodiment of Amaterasu, clans who were subservient to them (either for social, religious, or military reasons) would gain status through their association with Himiko's Uji-Gami. This transmission of power, from God, to Emperor/High Priestess, to vassal Clan is the foundation for all political legitimacy in Japan until the end of WW2, and even after the Emperor was stripped of his Godhood he was placed as a quasi-religious symbol of Japan's "Unity" in the first line of the post-war constitution. This is how important this sense of continuance from Japan's mythical roots is even today. Another thing to consider was the purpose of some of the Taika Reforms that accompanied this effort to legitimize this new style of government. The reforms introduced standardized taxation, the mustering of armed forces, and a re-organziation of the government to an extremely bureaucratic level. But some of the most important reforms are those around how titles are appointed, what titles now existed, and the methods of bestowing titles and badges of office. We can assume from the detail and specificity of this part of the decrees that the ability for any major family to assign themselves title was a becoming problematic. Association with Himiko may have introduced uncertainty into the new order, but this is admittedly speculation. However, there may be something to be said about the events that led up to the reforms themselves. Without getting too deep into it, the introduction of Buddhism and other benefits of the Tang (literacy and bureaucracy especially) had been met by significant resistance by the entrenched priest class Clans, who felt that Buddhism was an attack on their Shinto values, the Gods, and the land itself (which is all sort of the same thing?). The synthesis between Buddhist and Shinto practice is in part a result of the political negotiation and conflict of this period.

What does this mean for Himiko? It's possible she was omitted because making mention of the previous system political legitimacy may not have been good politics. It's possible she was forgotten, since she likely lived around 400-500 hundred years before the Nihon Shoki was written. I've even heard some discussion in a seminar I attended that posited Himiko (or at least SOME High Priestess) has been conflated with Amaterasu in the Nihon Shoki as Jimmu's relative. This is an interesting theory, but regrettably has no real way of being proven. It's even possible in this new patriarchal Confucian society that Shotoku was trying to build it would be unacceptable to pay deference to a Queen (though it is known he adored his mother, the Empress Suiko, this doesn't always translate elsewhere).

TLDR: The most likely reason is that by the time any one bothered to write anything down, Himiko was no longer relevant to who they thought was important.

EDIT: It has been pointed out quite correctly that I have forgotten that Himiko is mentioned a few times in the Nihon Shoki and is possibly conflated with the Empress Jingu. My specialty is in the re-opening of the country period through to WW2, so I apologize if I led anyone astray. However, I believe my point still stands that Himiko isn't really understood by those writing the Nihon Shoki and was not likely relevant to their goals when writing it.

EDIT: Thank you for the Gold! I will use it as inspiration to finally do a write up about the crazy 1860s and the Shinsengumi. I have also edited a few points because I accidentally forgot a word.

[Relevant Reading]

Sansom, George B. Japan - a short cultural history. Tokio: Tuttle, 1983.

Hall, John Whitney. Japan from prehistory to modern times. New York: Delacorte Press, 1970.

Muraoka, Tsunetsugu. Studies in Shinto thought. Tokyo: Japanese National Commission for UNESCO, 1964.

Brown, Delmer M., Kozo Yamamura, John Whitney Hall, Marius B. Jansen, Peter Duus, Donald H. Shively, and William H. McCullough. The Cambridge history of Japan. Cambridge: Cambridge University Press, 1993.