Wouldn't provide the emissary bonus. Purely a cosmetic feature. But I think it would be cool if after you sink an emissary ship and take their flag, you had the option to fly it off the back of your own boat (or pin it to the hull or something) to serve as a warning to others. Every time you sink a ship, you add a flag to your boat. You see a ship heading your way with 6 emissary flags already flying off the back of their ship, you'd know you're in trouble. But also you could be advertising yourself as a valuable target for reapers.