If they are misinterpreted, it is because the character encoding is not declared properly.

I still sometimes see mojibake in Japanese web pages, but sometimes it works; if it works, it is because the character encoding is declared properly.

In my opinion, EUC-JP is a generally better encoding of JIS (especially in e.g. C source code, which should not use Shift-JIS but EUC-JP is OK), but Shift-JIS does have some benefits in some circumstances (such as making a character grid with one byte per character cell; if using Shift-JIS for a Pascal source code then you should use (* *) instead of { } for comments please).