I think a lot of this is because, especially historically, people outside Czechia etc didn't know how to type Š. It's an effect of English-speaking countries defining global standards for computers, aviation and so on.

Hypothetically, and with a little exaggeration to make the point, if Sweden had somehow had that global influence in the mid-20th century, the American actress "Raquel Welch" might have been stuck with "Rakuel Velch" in her passport, and Swedish people would wonder why she was annoyed by this.