WSL processes are out of ConEmu control. Ask Microsoft to change implementation.
Please vote here feedback-hub:?contextid=268&feedbackid=099e4bf9-e6a4-486f-9d73-0340e6ed3997&form=1&src=2
Perhaps this helps? I used to turn off the system beep http://superuser.com/questions/10575/turning-off-the-cmd-window-beep-sound
Since the other solutions didn't work for me (for example, net stop beep got stuck like this forever: The service is starting or stopping. Please try again later.), the way I disabled the beep/ding in Cmder/ConEmu was by setting the sound for Critical Stop to none in system Sound settings.
No more dings!
For others that land here by search, the first two answers to Disable beep of Linux Bash on Windows 10 were the most helpful to me. In summary, handle it in linux/bash, not ConEmu:
Tab completion bell: edit /etc/inputrc
set bell-style none
Vim bell: edit $HOME/.vimrc
set visualbell
Most helpful comment
For others that land here by search, the first two answers to Disable beep of Linux Bash on Windows 10 were the most helpful to me. In summary, handle it in linux/bash, not ConEmu:
Tab completion bell: edit
/etc/inputrcVim bell: edit
$HOME/.vimrc