Update: Like Mario shooting out of a warp pipe just in time to save the Mushroom Kingdom, Nintendo has rolled out a new Nintendo Switch update meant to fix these HDMI audio issues (as well as other HDMI problems). Make sure your system's updated to version 4.0.1 and your sweet sound setup should be back in shape with plenty of time for enjoying the new tunes of Super Mario Odyssey.
Original story: Nintendo Switch update 4.0 added video capture and more good stuff to the system, but it also came with some new sound troubles. After installing the latest update, some Switch owners report choppy audio or no audio at all when playing games in docked mode. Crummy timing - Super Mario Odyssey, Nintendo Switch's biggest exclusive game yet, is set to arrive on Friday.
Looking through dozens of reports on Nintendo's official support forums and on Reddit, the issue seems to affect users who pass their Switch's audio through an extra piece of hardware before it goes to their speakers, such as an AV receiver or HDMI audio extractor. Not everybody with this kind of setup is being affected but enough are to present a clear pattern.
At the moment, the only official response I've seen from Nintendo was posted by a moderator on the support forum; the mod recommends Switch owners who are experiencing this issue to call or chat with the Nintendo Support line directly. Feel free to do that, but don't expect instant resolution. This looks like something Nintendo is going to have to fix on its end.
From the reports I've seen, docked audio should work fine if you can play your Switch's audio directly through your TV speakers. Update 4.0 also handily added support for wireless USB headsets, so there's another option. But it would be a serious bummer to listen to Mayor Pauline and the citizens of New Donk City perform "Jump Up, Superstar" in anything less than optimal sound quality. Hopefully Nintendo puts out another update to fix these issues before Mario makes his grand return to 3D platforming.