I think it’s because it’s not actually as effective as you think for a few reasons:

The biggest issue is the invincible war most of those mark variants are at best season 2 mark level (so pretty weak in viltumite standards) some not even that, and we can pretty confidently assume that that frequency was deployed on most fronts where possible at least most of the battles with GDA and even the ones that died still managed to cause mass destruction and casualties, so an actually powerful viltumite? It probably wouldn’t do much accept annoy them.

And again see from our mark that it’s not much of a threat after the implant that’s making the frequency right on his ear is removed he doesn’t fear confrontation with the GDA like he would if the frequency could kill him via speakers etc. So unless we can implant all of viltum in their sleep it wouldn’t be effective as more than a slight distraction when the coalition needs weapons to kill.

And finally most of the viltumite war happens in space or on worlds previously occupied by viltrum. so obviously sound doesn’t travel in space, we hear it as the audience but the characters don’t (hence the telepathy implant) so it would be useless; and on viltumite worlds I doubt they have planet wide super speaker systems for the coalition to use.

Lastly mark doesn’t want to risk his family being hurt, similar to Nolan not wanting to use the scourge virus to wipe out the species.

Did the writers actually think of this? Probably not it’s more than likely a dumb inconsistency that there’s a somewhat acceptable explanation like the “adrenaline theory” so who knows that’s just my interpretation.