Simply, it's because musica is a feminine noun.
As to why it might be plural, which is a separate question really, it seems here to mean something more akin to "musical arts." This isn't really a Classical development, but was probably what the founders of the TML had in mind when they founded it, especially given it's mission:
The Thesaurus Musicarum Latinarum (TML) was created in 1990 by the initiative of a group of scholars from around the world, under the direction of Thomas Mathiesen at Indiana University, with the ambition to collect in electronic format the entire corpus of Latin music theory written during the Middle Ages and the Renaissance.
These texts are literary works that discuss general principles (e.g. the origin and nature of music, its role within human activities) or technical issues (e.g. the construction of musical instruments); or describe or define procedures (composition, notation and performance), and genres or styles (within liturgical, secular, and instrumental repertories, in monody and polyphony).
So it's not about musicians or even songs per se, but the multitude of theories and arts that go into the creation of Latin music.