The function PlaySoundFile() receives 2 parameters: the audio to play and the audio channel to use. If you check the audio channel options, I'm using "Master", which plays the sound even with disabled sounds (ambience, music or other effects such as abilities). In theory once you disable the audio "CTRL + S" and the music "CTRL + M", you shouldn't hear anything else other than sounds played from the Master channel.
You can test it easily by disabling music and sounds effects and flying over Nagrand (looking for the elite rares in that place). You should be able to hear only Rarescanner alerts.
It uses the general sound channel, which you can hear even if you disable the sounds/music of the game or minimize it (in window mode with Sound in background activated). So you can always disable the sounds in wow, and you will still hear an alert if you find a rare while you are doing something else.
That's new, it only asked me once, and now everytime I click on the button it doesn't show up. I just tried again with a couple of characters and it didn't pop up. I will keep looking into this anyway.
I've been researching about this issue and there's not much I can do.
In order to target and mark a NPC I need to use scripts because the API methods are protected, which means we cannot use them in an addon (only the game is able to), I forgot that's why I did it like this in the past :)
Perhaps with time Blizzard will whitelist inoffensive scripts like "/target" and you won't see the message again.
Anyway, if you see it, you can accept clicking "yes" and you won't see it again.
I also noticed that warning, however I cliked "yes" and everything worked fine.
It's a new warning message added by Blizzard to inform about the use of scripts in addons, if you check the wow site forums you will find a lot of people asking about these warnings while using different addons and macros.
I will take a look into this, perhaps there is a new method to mark NPCs without using scripts.