All languages change and evolve over time, and Japanese is certainly no different. There was no written language in Japan until kanji was introduced along with Buddhism and Confucianism around the 5th century. At first Chinese kanji were used directly, with Japanese grammar and character pronunciations more or less laid on top (a system known as kanbun), and this was replaced by a system of assigning sounds to characters arbitrarily (the man’yo-gana), which grew into the hiragana and katakana writing systems in use today. But the Japanese language has continued to change even in recent years. For example, the current practice of writing Japanese horizontally from left-to-right was only standardized after World War II, and if you look at the “retro” design on the Sakuma Drops candies, you might be able to tell that the writing is “backwards” compared with how the language is written today. There are several hiragana and katakana characters that were commonly used a century ago but which have disappeared from use today…although Hideki Anno goes out of his way to design all written text in Evangelion to use these strange, archaic characters as much as possible.
Evangelion is filled with bizarre, archaic writing just to be different.