Loaded full of metal pellets.

You make a good point with flare guns, but I wouldn't be terribly afraid of them. Maybe someone on a plane could cause a lot of panic with flare gun but that's not much different that causing a fire with other means. You might be able to kill someone with the initial shot, but that's it.

In a shotgun shell, the pellets (or slug) and primer section are still metal. You couldn't smuggle a shotgun shell through a metal detector any more than you could smuggle a regular bullet through.

The shot, however, is not plastic.