After upgrading the Shield TV to NVIDIA experience 5.0.2, Plex updated to 5.4.0 and worked great. After updating to 5.4.1 passthrough audio stopped working. I uninstalled all updates and the version that shipped with 5.0.2 worked. I downloaded 5.4.0 and sideloaded it and that works great. Then I manually updated to 5.4.1 available on the Google Play store, and passthrough was broken again.
I uninstalled all updates and sideloaded 5.4.0 again and audio is back to working.