I haven't looked at the data sheet, but most logic-controlled audio switches use a single supply, hence the need for decoupling caps, so yes there could be some noise associated with the DC offset switching. It depends, and there's often text in the app notes detailing how to deal with this.
Most of these ICs use zero-crossing detection to avoid pops from the audio signal itself. But again, this is a quick reply and I haven't read the data sheet to verify.
That said, I can't help but feel there has to be a better approach than this. OP: Would you be willing to detail more on the implementation of your instrument?