True, with his shooting he maybe stopped them from taking Robin.
But they don't get a bounty because their mission was a success. They get a bounty for destroying and attacking the island and WG and for beating CP9.
Shooting a flag isn't that great. But did he shoot it on his will or did Luffy tell him to shoot it? (can't remember)
If Luffy told him to do it, he'll get credit for it since it was done on his will.
And we shouldn't forget that only one strawhat didn't defeat a CP9. And that was Lysopp. Nami and Chopper on the other hand did.
"For Feanor was made the mightiest in all parts of body and mind, in valour, in endurance, in beauty, in understanding, in skill, in strength and subtlety alike, of all the Children of Illuvatar, and a bright flame was in him"