That's Alastair Reynolds "Century Rain" (my personal favourite among Reynolds' novels). The war is between two human factions - "Threshers" (derived from "threshold", since they don't allow technology beyond a certain level of complexity) and "Slashers", who embrace nanotechnology. Earth was an early casualty in their conflict.
No aliens per se, but Alien artifacts (artifical wormholes, copies of planet Earth).
Haven't the book with me, but e.g. this review specifically mentions the "amusica virus" (strange review by the way, since music actually has a big role in the novel). Also this one.
Made it even into TV tropes (there goes the rest of your day):
Dreadful Musician: Averted in Century Rain: in an early scene the
protagonist is walking into a superior's office while he plays a
violin, with her Internal Monologue noting how grating and painful the
music is. It is then revealed that she, along with a large portion of
the rest of the human race, were infected with a designer-disease
called 'amusica', which prevented people from enjoying music, to ruin
their side's morale. After all, someone who can't appreciate music
can't get patriotic fervor from their anthems, now can they?