Yeah, I agree that a GUC for this is quite unappetizing.
How would you feel about a variant for calling NOTIFY?
The SQL syntax could be something like "NOTIFY [ALL] channel, payload" where the ALL means "just send the notification already, nobody cares whether there's an identical one in the queue".
Likewise we could introduce a three-argument form of pg_notify(text, text, bool) where the final argument is whether you are interested in removing duplicates.
Optimising the remove-duplicates path is still probably a worthwhile endeavour, but if the user really doesn't care at all about duplication, it seems silly to force them to pay any performance price for a behaviour they didn't want, no?