freeShop has new music playback settings. It can play music directly from eShop’s extdata or using user-provided audio files. Format support will be BCSTM (DSP ADPCM), Ogg (Vorbis), and basic AAC. It is recommended that you use BCSTM format. There is a great community for music in this format found here: http://smashcustommusic.com/
Will be available for testing within a couple days.
The new directory for audio files will be sd:/3ds/data/freeShop/music/. There is no support for subdirectories currently, so only the files directly there will be usable.
You will notice an /eshop/ subdirectory there, but you should just leave it alone. That will have eShop audio files, and it will be auto-created if you try to remove it.