The USCG requires flares... Not FLARE guns. There are several options for signal devices that do not require the actual(in most cases worthless) flare gun.
The following illustrates the variety and combination of devices which can be carried in order to meet the requirements:

Three hand-held red flares (day and night).

One hand-held red flare and two parachute flares (day and night).

One hand-held orange smoke signal, two floating orange smoke signals (day), and one electric distress light (night only).

All distress signals have distinct advantages and disadvantages. No single device is ideal under all conditions or suitable for all purposes. Pyrotechnics are universally recognized as excellent distress signals. However, there is potential for injury and property damage if not properly handled. These devices produce a very hot flame and the residue can cause burns and ignite flammable materials.

Pistol launched and hand-held parachute flares and meteors have many characteristics of a firearm and must be handled with caution. In some states they are considered a firearm and prohibited from use.

There are a number of places where getting caught with a flare GUN could cause those aboard legal issues. It is best to never have those on a boat. One of these could lead to your arrest on firearm charges...