It will/won't.
For SSB3DS to load mods such as custom textures or skins, it is required that you either use a modified code.bin or a repacked dt/ls file. The dt/ls file can be unpacked but not repacked. However, music mods and the such can be used with layeredfs, however it is easier to just do the whole thing via SaltySD.
Like others have said, use the modified code.bin and then you are golden. There is no point in using LayeredFS.
Download the code.bin, put in the right place, then use saltysd.
That answers your question.