My own personal inclination devoid of any other considerations would be to elongate the vowels, yes.
But for established place names of modern cities it just seems less pressing, given that there's less support for it - and even I type "Tokyo" instinctively, despite knowing better and despite making a concerted effort to always elongate my vowels and be consistent in my romanization. Even in casual conversation completely unrelated to Danbooru.
So... ehhhhh, this isn't something I feel strongly enough to push without wider support. Certainly not for Tokyo at least. I'm a bit more willing on other cities (only a handful of which will ever come up as issues).