To programmatically acknowledge or handle a "missing audio device" popup in macOS when using Audio Hijack, you can use AppleScript or a shell script to automate certain responses, though there are limitations depending on the nature and context of the popup.
osascript -e 'tell application "System Events"' -e 'tell process "Audio Hijack"' -e 'try' -e 'click button 1 of (first window whose subrole is "AXDialog")' -e 'end try' -e 'end tell' -e 'end tell'
You may Save this as a .scpt
file and run it with Script Editor or osascript
from Terminal.