I've had the same happen as well, and it gets worse when there are other entities such as weevoles and vampire bats on screen en masse to the point that I was at single-digit FPS. Manually turning down instances of tall grass and weevole/bat spawns helped but I'd rather not have to do that...
When shadow hands disappear at the end of a night while indoors (i.e., inside the purchasable home), the music box jingle continues to loop not only in the player home, but also in all other enterable structures in town. The sound also persists in other enterable areas including Cave Clefts, Mant Hills, and ruin entrances. The passage of time doesn't appear to stop the looped sound as well, as 2 days have passed between the start of the sound looping.