If the extraterrestrials were at the core of the Nazi regime in Germany, aiding the German war effort, why didn’t they help the Germans develop an atomic weapon? Did they not detect what America was doing with the Manhattan Project?

They were aware of the human war effort but underestimated the success the Americans would have in being able to produce an atomic weapon successfully. The reason they did not help the Germans do so is they simply did not want to so heavily contaminate the planet with radioactive fallout given their wish to be able to navigate smoothly planet-wide to continue doing their managing of the human population and its doings. And while this was geared towards annihilation, they wanted to have free rein to come and go themselves directly, as well as to protect others assisting them, including the human bloodline in positions of power and authority across the world, so it was simply not their highest priority to see that humans in any locale develop advanced atomic weaponry. Once this had been done, however, they took advantage of this to continue playing their games and this led to the famous Cold War scale-up of nuclear armament by the opposing factions of Soviet Union and the United States first, and then by a series of jealous nations to spread the accumulation of atomic weapons of various kinds, and this continues to the present day. Depending on their mood and their particular plans, they may or may not allow nuclear war to happen. It would depend on the timing and the particular series of events creating this possibility as to whether it would be supported or suppressed, at least for a time, to allow other plans to hatch, and other plans to come to fruition, and follow a preferred order of events.