Cold war? I assumed Manhattan Project was taking place in the middle of a world war.
You are correct. During WWII, allied powers did in fact bomb and sabotage German facilities known to be important to the German atomic bomb project (called "Uranprojekt")
In the sequel to the game, The Manhattan Project 2: Minutes to Midnight, which takes place during the Cold War, I did choose to leave out the air strikes in part due to thematic reasons.