Heller was even with the same squadron 488-th, but he was assigned to it on 21-st of May 1944 so a few months after the collision - see below (on a side note, check the last name in the list of the assigned on that day! This is the name that inspired him for Yossarian. ):
Heller uses the mission on Sept. 23, 1944 (when 488-th and 489-th BS bombed the cruiser "Taranto" in La Spezia) for the deaths of Dobbs and Nately, but it's quite possible that he learned about the mid-air collision in the squadron or even studied it in detail after the war.
Copied from "Historical Sources for the Events in Joseph Heller's Novel, Catch-22" by Daniel Setzer
Cheers!