Nihombashi, a district of Tokyo, has long been spelled with “m,” instead of “n,” although the consonant is followed by “b.”

Apart from the punctuation following crazy American rules going really really wrong here, the sentence does not make any sense, at all. You'll see Nihonbashi like 9 out of 10 times on the street and on the maps. Nihombashi is a minority spelling; it is indeed truer to the sound of it as the moraic nasal (written ん as in にほんばし) is not an [n] but rather an "underspecified nasal closure" than can come out as [n], [m], [ŋ] or even a sound approaching [b] depending on the surrounding sounds and the speaker. But it's a usage only followed by a minority.

Now the article says the place name has long been spelled with "m" instead of "n"—not true—and remarks that that is "although" "n" is here followed by "b"—that's wrong, the "m" is used here because the nasal precedes "b", it is a case of retrograde assimilation.

Lastly the article tries to concoct a newsworthy soup out of a bit of thin air that escaped out of a bureaucracy concerned with its own relevance. Be it said that for decades nobody except some nerds, some die-hards, some spelling enthusiasts and unhappy people forced to obey a particular set of arcane rules set up after the war has been, in the past half-century, publicly written "Hukusima" or "zyûdô" in earnest. These are totally cromulent and systematic spellings when you know the system and they're true to the Japanese phonological system, but nobody uses them. The news here is that, maybe, in the future, even fewer people may be using them, and that those who ditched the rules that only applied to some government agencies anyway can now do so without breaking the rules.