Well, it's like this: Danbooru, like most English fan communities of Japanese media, uses a waapuro ("word processor")-derived modified Hepburn romanization system for writing Japanese words in Latin characters. This system is used because:
1) Pronunciations are generally more intuitive for English speakers, compared to Kunrei-shiki.
2) It preserves the distinction between short and long vowels.
3) It avoids the use of macrons and circumflex accents that can be difficult to input on a standard (US) keyboard.
4) It is a more regular system (compared to some other Hepburn variants). Instead of trying to figure out whether to transcribe う as 'u' or 'o' or 'h' (depending on the preceding 'vowel'), all one needs to do is to transcribe the same kana directly into the same Latin letters. So う is always 'u".
For similar reasons, other fan communities (Touhou in particular) also tend to use the same or a similar romanization scheme.
Some exceptions are of course made for words that are often romanized in a different style. So, Tokyo instead of Toukyou and Kyoto instead of Kyouto. Likewise, for fictional characters or other words, we tend to also follow what their respective fandoms (or in-communities/subcultures) use, so as to maintain consistency in naming. So, we get Tohsaka instead of Toosaka, Tohno instead of Toono, Azumanga_Daioh instead of Daiou, Yu-Gi-Oh instead of Yu-Gi-Ou, and Shirow Masamune instead of Shirou. This helps us preserve consistency with the terms and names used in their respective fandoms, making it easier and more intuitive to search and tag them.
Now, our 'in-house' romanization scheme has been revised recently (as per topic #17011) to allow for more 'institutional flexibility' regarding this issue (i.e. gives us a justification to say "da rules allow this", instead of needing to go "let's make an(other) exception for this, because reasons"), but the default romanization scheme is still this waapuro-derived modified Hepburn. That is why most of the characters/copyrights with 魔王/まおう in their names have it translated as "maou" instead of "maoh" like what you would expect from Azumanga Daioh and Yu-Gi-Oh, despite having the same 王/おう ending.
Going back to fan-preferred romanizations... generally speaking, the author or copyright holders (or 'official' localization teams) has siginficant sway in this. If a copyright manages to 'establish' a specific way of writing a particular name (or term), then most fandoms will follow that convention, and Danbooru will follow likewise. This is also why we use localized names for Pokemon and Fire Emblem characters. Again, the same reason applies; it makes it easier for users to recognize those tags and search and tag them.
As another example, for Umamusume in particular we tend to use the official JRA spelling instead of our default romanization scheme because the characters are based on real-life horses with long established names that have already been spelled in a certain way in English for ages because of, well, the horse racing industry (and newspapers and other news sources documenting said industry).
And on a related note, to extend the analogy with a Chinese example instead of a Japanese one, Arknights characters and terms with Chinese names also use Wade-Giles preferred in the localization (Ch'en instead of Chen) instead of Pinyin romanization which we use as our default 'semi-official' scheme elsewhere. Reason being, of course, that the Wade-Giles romanizations have become firmly established among the English fandom.
Sometimes there's a pushback, with fans rejecting 'official' names. Most notably this tend to occur for Type-Moon copyrights, with Altria/Altoria being the most prominent example. Fans just prefer some other spelling for their names and we follow likewise.
For works that are less 'in the spotlight', less marketed towards the English-speaking community, usually the first names people will hear off is going to be a romanization from a fan-translator, and these people tend to use the same waapuro-derived modified Hepburn system we use (main possible deviation being 'oh' vs 'oo', because spelling 'oo' tends to cause people to mispronounce it). Touhou names and terms in particular gets translated by the Touhou fandom pretty fast, and again, as mentioned, they use the same default convention as us, which is how the spelling "Fujiwara no Mokou" got solidified in the Touhou fandom and on Danbooru.
TL;DR: We have a consistent romanization system for romanizing Japanese names and other words; we tend to stick to this convention unless there's a good reason to make an exception (i.e. nearly all other people spell it in another way), the Touhou fandom tends to use the same default romanization system as us (because, really, we more or less started off as part of the same 'community' anyway), Fujiwara no Mokou is how nearly every single English speaker spells her name... and -1 to your proposal because it just introduces an arbitrary inconsistency all for no good reason.
