SMuFL is a font layout specification. It solves the longtime problem of "I'm making a music font. Which Unicode code glyph should I use for a treble clef?" For many years, this was a Wild West situation, and it wasn't possible to swap music fonts because they defined their glyphs in inconsistent ways. This problem is basically solved now, thanks to SMuFL.
MNX is a way of encoding the music itself. It solves the problem of "I have some music notation I want to encode in a semantic format, so it can be analyzed/displayed/exported/imported/etc."