So, since the beginning of time Danbooru has used japanese names as tags. I personally think that this rule is kinda outdated: I don't really know about anime, but a lot of games usually have the japanese names either untouched, translated or localized. Since the english version is usually more famous than the japanese version (if the english version came out at the same time as the japanese version), i think that there should be an addendum to the ''using japanese names over english names'' rule: ''If the english localization came out at the same time as the japanese version, the english version should be used''. This is mainly because of consistency: some games have both english and japanese name tags (example: Fire Emblem has half japanese names half english, and i personally think this is unacceptable). topic #15691 is an example of why using translated names over unofficial romaji is a good thing (example: the unofficial romaji according to Danbooru rules of the character Elisanne should be Erufirisu, which doesn't really roll off the tongue).
On anime: I think japanese names are better in this case, since most of the time localization isn't made by the company that made the anime.