I noticed 3rd problem. So, I'm adding the info here. Before describing it, I describe first 2 problems.
1. Japanese APL tag information (song/artist/album names) appear strange in MC9. If I use new MakeAPL and create UTF-8 tagged APL files, there is no problem.
2. Any APL files inside a directory using Japanese character (encoded by SHIFT-JIS) lose tag information in MC9. MC9 shows song/artist/album names as unassigned. This will be fixed once APE plugin stop parsing file path or something, I hope.
3rd problem is the same problem as the 1st. I noticed MC9 is converting SHIFT-JIS encoded tag information in old APL files into UTF-8 indeed. However, MC9 shows UTF-8 converted string as SHIFT-JIS. It was the reason why I saw strange string. I guess MC9 internal string has a bit to say this string is Windows native string or UTF-8 string. And I imagine APE plug-in read Windows native string and convert it into UTF-8, but forgot to set this bit. I wish this help to make MC9 work well either new APL files or old APL fies.
And one more internationalization probelm is... (this is off topic from APL tag thread though) MC9 doesn't convert cdplayer.ini information to UTF-8.