A couple reasons I'm aware of:

- Han unification. Chinese and Japanese characters that have the same etymology but are written differently are sometimes assigned to the same codepoint, and it's up to the font to distinguish. And application designers... tend not to detect the language and change the font accordingly. This leads to Japanese text being rendered in a Chinese font.

- Some Han de-unification has happened in Unicode now. Great. Which version should fonts and encodings support?

- Nobody actually knows the complete de facto mapping between Shift-JIS and Unicode. Yes, there are standards and ICU and Python modules and stuff; they're incomplete. This leads to data loss surrounding rare characters.

(Tell me you've got such a mapping and I'll give you some strings I found in the wild to decode with it.)

One legitimate concern I know of for email is that you could still get Japanese mobile phones as late as 2008 that didn't support UTF-8. People setting their mail filters to autotrash UTF-8 has also definitely happened (pro tip: never attempt to filter by charset; if you really want to, filter by script instead).

I believe another major issue is that a fair amount of software sets language environment for things such as fonts based on charset. Charsets such as ISO-2022-JP, GBK, and Big5 give you a clear clue as to what the underlying language is, but UTF-8 just tells you "here is CJK ideographs, good luck!" On the other hand, I've never really heard of any opposition to Unicode from Chinese or Korean locales, so I suspect a large part of it is just stubborn tech entrenchment in Japan as opposed to strong technical reasons.