The full phrase is "yet well I know that music hath (has) a far more pleasing sound". The verses make it slightly confusing; you need to read it as "I know that..." instead of "that music hath..." (this music, which music).

Hi here is an analysis of Sonnet 10. My mistress' eyes are nothing like the sun; My mistress's eyes are nothing like the sun; Coral is far more red than her lips' red; Coral is far more red than her lips; If snow be white, why then her breasts are dun; If snow is white, then her breasts are a brownish gray; If hairs be wires, black wires grow on her head. If hairs are like wires, hers are black and not golden. I have seen roses damask'd, red and white, I have seen damask roses, red and white [streaked], But no such roses see I in her cheeks; But I do not see such colors in her cheeks; And in some perfumes is there more delight And some perfumes give more delight Than in the breath that from my mistress reeks. Than the horrid breath of my mistress. I love to hear her speak, yet well I know I love to hear her speak, but I know That music hath a far more pleasing sound; That music has a more pleasing sound. I grant I never saw a goddess go; I've never seen a goddess walk; My mistress, when she walks, treads on the ground: But I know that my mistress walks only on the ground. And yet, by heaven, I think my love as rare And yet I think my love as rare As any she belied with false compare. As any woman who has been misrepresented by ridiculous comparisons.

"Hath" means "has," so all this means is that that music sounds better.