There are some rather advanced statistical models and method in musicology (e.g., Beran's Statistics in Musicology or the edited volume Mathematics and Composition in Music). There's even a volume Music that Works which incorporates everything from neurobiology to cognitive development. However, my knowledge of musicology is quite limited (it's my brother's field, and his research concerns history, not mathematics). On the other hand, I have a background in classics, and the ancient Greeks began the "mathematical" approach to scales, chords, and harmonics. That said, there is nothing about the nature of music or harmonic analysis which makes these somehow fundamental components of reality. The quantitative analysis of tones, cords, etc., has to do with
1) fuzzy cuts/slices to produce crisp sets
2) interpretation of perceptual input and a categorical analysis which reflects a sensory-based construction, not any fundamental components of reality.