*UPDATE*
This is version 2 of The Legend of Zelda Majora's Mask 3D - No Music mod. It is made for the USA v1.0 rom of MM3D. This mod is a vast improvement over the earlier version in every conceivable way. For one, the xdelta patch files are way smaller than those of version 1, and can be downloaded straight from this RHDN page, without the need to use any links from external file hosting sites. Two, it is able to mute ALL of the BGM for both original hardware and emulator. Even those songs that would cause the 3DS to crash in the previous version, are now muted in this improvement. Three, this mod is able to mute the Grezzo ending credits for both original hardware and emulator, which would cause a softlock for both in the previous version.

As stated before, jingles such as the ones that play when you get an item, get a heart piece or container, get a mask, beat a race, the playback for ocarina songs, the Zora jam sessions, the Frog Choir, and the Ballad of the Wind Fish Milk Bar song playback have not been removed, in order to maintain the character of the game. The flute that plays Saria's Song in the ending credits will appear.

There are 2 separate xdelta patch files. One is labeled 3DS, meaning that it is meant to be used to patch a .cia file of the game, which can then be installed on a modded 3DS console. The second xdelta patch file is meant to be used to patch a .3ds file of the game, so that it can be used in an emulator like Citra. Please don't be confused by this explanation. .3ds files are for emulators like Citra, and .cia files are for original 3DS hardware. Also, be sure to backup your Majora's Mask 3D save file on your 3DS, if you have one, because installing a new .cia file of MM3D will wipe over the old one and its save data.

This mod is 100% compatible with the Majora's Mask 3D Project Restoration hack.

The original description is provided below for reference and to maintain a record of the change.
*UPDATE*

*ORIGINAL DESCRIPTION FOR VERSION 1.0 OF THE MOD*
This mod removes the background music in The Legend of Zelda Majora's Mask 3D. Jingles such as the ones that play when you get an item, get a mask, beat a race, the playback for ocarina songs, the Zora jam sessions, the Frog Choir, and the Ballad of the Wind Fish Milk Bar song playback have not been removed, in order to keep the character of the game intact.

There are 2 versions of this mod, one is for Citra, and the other is for original 3DS hardware. Keep in mind, when making the rom with XDeltaUI, include the extension .3ds for the Citra version and .cia for the 3DS. Don't let this last step confuse you. Also, be sure to backup your Majora's Mask 3D save file on your 3DS, if you have one, because inserting a new .cia file of MM3D will wipe over the old one and its save data.

The Citra version removes all of the background music (except those mentioned above), whereas the 3DS version does not remove the shop music nor the boat cruise music, because removing either of these 2 tracks will cause the 3DS to crash. The flute that plays Saria's Song at the ending credits will appear in both versions. The Grezzo ending credits music could not be removed from either version. This mod is 100% compatible with the Majora's Mask 3D Project Restoration hack.
*ORIGINAL DESCRIPTION*