What was used for conversion?
I don't think it matters, MP3 is LOWER quality than AAC per that article you posted, so you can't UP an MP3 to that AAC standard, you would have to go back to source media (music CDs) and make the AAC's directly, that is the problem.
NOT POSSIBLE with inferior source MP3's in a nutshell.
How others dealt with this perhaps check in a Nintendo DS forum.
AAC rippers exist though, assuming you have some actual CDs.
I don't have a 3DS, maybe there have been some discovered tricks, seems pathetic if they don't play mp3s.