I'm interested to see your specific question doesn't seem to have come up before. It was partially covered by /u/ParkSungJun, who answered How was the ideology of Imperial Japan so compelling? by explaining that kamikaze pilots generally did not believe anything related to Shinto, religion, or the emperor. He didn't give a citation, but Emiko Ohnuki-Tierney's book Kamikaze Diaries: Reflections of Japanese Student Soldiers (2007) gives a raw and scintillating look into what pilots really believed.

More generally, you have merged together several things here.

• Yokai don't have anything to do with WW2. Please check my earlier answer about how yokai were "spiritualized" in the 19th century. In the 20th century, they were even further displaced from normalized human interaction and don't belong in this question.
• Hirohito was not considered invincible. The most common belief was that he was a descendant of a divinely authorized 2600-year unbroken line, unlike any other dynasty in the world, and that the nation of Japan had a collective mission to protect him and his family (his son Akihito, a child at the time, just recently retired as emperor). Hirohito's life could be more important than one's own life. The media created a massive cult around this. But many people didn't believe it! Just as important as manufacturing belief was silencing dissent, and creating an environment where it was unsafe to share your skepticism. Calling the emperor an ordinary human was grounds for shunning or even arrest, not on the grounds that he had superpowers, but because he was supposed to be the most irreplaceable person in the country.
• Japan refused to surrender mainly because of propaganda that Americans were violent, racist barbarians who wanted to rape and kill every Japanese person down to a man. This propaganda was generally effective because it appealed to Japan's preexisting xenophobia. Within this propaganda was a desire to "protect the emperor" but it was kind of self-serving, with the "emperor" being a stand-in for military elites who wanted to protect themselves. The Kyūjō incident is proof that the actual desires of the emperor didn't matter much to those at the top.

What exactly is "Shinto" here? Actually this was an open question in 1945, Shinto being a very vague term. Japan would have it that Shinto was just a non-religious style of venerating famous men and women that even Christians could participate in. America disagreed, and in 1947 they declared Shinto a religion. The Emperor's claim to divine authorization was grounded in ancient history books; after 1947, this history was declared mythology associated with the newly defined religion of Shinto.