"Shooting a red emergency flare in the USA without prior permission or in an emergency is illegal." Not that I doubt you, but if it is illegal on a federal level, perhaps there's a citation from the USC or CFR you can give us to back that up?
"The USCG, ATF and homeland Security do not consider them [flare guns] to be a “fire arm”" Yeah, but we're not talking about them, we're talking about local, county, and state PDs, and they'll tell you "tell that to the judge" while you're being arrested. In many states a "firearm" is in fact defined in the state laws and usually it is defined alng the lines of "any device which fires, propels, or launches a projectile by any means of stored power, including springs, explosive charges, compressed air or gas..." and yes, you just try carrying one in front of a cop in DC or NYC. It's a GUN in both places, although at least in NYC if you are not displaying it, but transporting it to or from a boat, they'll ignore it. Be seen with it in your hand in a parking lot--and you can tell it to the judge.
And if you think Homeland Security's TSA section is going to allow you to carry it, even unloaded, onto the cabin of a commercial airliner...don't think so. I'd sure like to be there when you try it.