A while back I wrote about silencing KDE application notification sounds under fvwm, where the solution was to open up the desktop settings or volume control application of your choice and turn off the volume of what is variously called 'Notification Sounds' or 'System Sounds'. Initially I did this through KDE and thought it was a KDE-specific setting, but as pointed out to me in comments, this is actually a global (to the system) sound stream for system sounds and events. This is an extremely blunt hammer to deal with unwanted notification sounds, and Linux should do better. In practice this means both programs and desktop toolkits, such as KDE and GTK.

Modern mobile devices show what's possible and what we should be able to get on Linux. Mobile OSes such as iOS support mandatory system level control over whether each application can use sounds (or other things) in their notifications. Better applications also provide granular control over what noises they may optionally make, including 'none'. Of course there's a place for a global control, but it should be your last resort if your issue is with a specific application making unwanted noises, especially for non-urgent things.

(Some people will want their computer to make no noises at all, but others may want to preserve some system sounds for, for example, urgent issues or alerts.)

The state in current desktops (in Fedora 37) seems somewhat mixed. Cinnamon gives you control over what sounds its desktop shell makes, but not over what notification sounds its applications generate (never mind applications from other desktops). GNOME, in its 'Notifications' section, offers specific controls over sound usage by notification by application, but only for GNOME applications. If you dig deep enough in KDE settings, KDE seems to have quite fine grained control over notification sounds from certain KDE applications, but this doesn't seem to include applications that are merely KDE-based, like kdiff3.

If GNOME's notification sound setting worked for everything, it would have basically the interface I'd want (and be very similar to what iOS and I believe Android support, which may not be a coincidence). However, achieving this would probably require everyone to agree on some sort of standard for notifications, either in the form of 'send your notification stuff here to a daemon that will actually make them appear' (and then the daemon could filter things), or for exposing and configuring notification settings for arbitrary programs.

Until such a beautiful day comes to pass, Linux sound notifications will continue to be an irritating mess and probably irritate people when some random program suddenly bings and bongs at them. The likely consequence of this is that more people turn off system sounds entirely.