We now know from Vegapunk that Joy Boy was the first to be known as a pirate. Going by the attitude of the World Government today towards the pirates, the 20 kings and Imu would have done all in their power to defeat Joy Boy both at war as well as his ideology of being the freest man on the seas. The most symbolic way to do the latter would be to burn his flag or the Jolly Roger in this case.
I believe that while they were successful in defeating him, as evidenced by the fact that Imu apparently has Joy Boy’s straw hat as a trophy, they were not able to erase his ideology as we still have pirates today. What I think happened was that they were able to destroy Joy Boy’s ship in the war but were not able to burn/destroy his Jolly Roger. So while the ship was destroyed, “one piece” of it remained and thus the name of the “treasure” as it symbolizes all that pirates live for. And that is what Imu and the World Government hate so much and are doing everything they can to prevent today’s pirates from getting their hands on.
During the run up to Laugh Tale, maybe the Straw Hats’ Jolly Roger would be damaged by the World Government and when Luffy returns from Laugh Tale, he is now flying Joy Boy’s Jolly Roger along with his own much to the chagrin of Imu and the World Government. And that could be a flag that the entire alliance against the World Government could rally to during the final war.
Judging by the fact that Luffy has inherited both his fruit and his will, if Joy Boy also “designed” his own Jolly Roger then it should be something wacky like the Straw Hat’s Jolly Roger which would explain why Roger laughed.
*Theory by the_bridgeburner
