Han unification has been overly aggressive about merging some characters, but the basic principle is not as flawed as it is some times (as in this article) made to sound. The vast majority of Japanese and Chinese characters are not only similar, they are identical. Not all are. Some are clearly different characters deriving from a common historical root, and should not be unified. Sometimes, when characters are a bit different, it is a matter of font. Out of the tends of thousands of characters used by these languages, it is not surprising that mistakes have been made, and yes, han unification has been a bit too far reaching. But not unifying at all would have been much worse. You don't want a in German and a in English to be different letters just because Helvetica and Baskerville look different.

Also, since CJK languages are comfortable with having an unbounded set of letters to work from, they tend to be comfortable with declaring every odd thing a separate letter. Witness the mess that half-width katakana is. Or notice that the origin of most emoji is not in the disregard of white old men for "lesser" languages, but comes from importing existing characters from Japanese encodings.

Which also hints at one more factor. Historically, and still very much to this day, Japan has been much more active in standardization bodies than most other non western countries. Unsurprisingly, Japanese is much better supported by modern software than many other non western languages.