@EmeliaK you lost me on a few of those references. Regardless, I can see your point, but when an official romaji spelling is given, I'm the type that opts to keep it, since, if I'm going to be trying to faithfully adapt someone else's work in the first place, I may as well stay faithful through and through.
I think it's also a matter of pronunciation, where in this case "Youko" makes people automatically default to saying "Yuuko" or "Yo-ooh-ko" rather than "Yoko".
In cases like Touhou, I've never seen Toho before, so I have always been under the assumption it's pronounced "Toe-hoe" rather than "To-ho", a very subtle difference, but noticable in speech via inflection.