Answer:
Several branches of musicology focus on scientific aspects. Music Cognition is an empirically-based and lab-oriented discipline that is considered part of musicology. The science of acoustics is also related to musicology. See the web site for the Society for Music Perception and Cognition (http://www.musicperception.org/) for further info.
For the philosophical perspective: many musicological works take up philosophical aspects of music (e.g. Adorno), and many philosophical works touch upon music (e.g. Schopenhauer). Many branches of musicology incorporate a philosophical perspective. You might find assistance on this area through the Music and Philosophy Study Group of the American Musicological Society (www.ams-net.org). The study group has a session at the upcoming annual meeting of the AMS. See http://www.ams-net.org/indianapolis/Indianapolis-Abstracts-Final.pdf, page 80 (Merleau-Ponty) or page 229 (Jankelevitch).