I'm going to pitch into this as I think most of the discussion is missing the point because we are ignoring the true nature of the Manhattan project, the actual practicality of others to create atomic bombs and what would be realistic affects of atomic bombs.
First of all, the really spectacular aspect of the Manhattan project once it started (and it was a bit late getting started) was the overwhelming expenditure on researching everything at once. If you look at it in some detail there are a whole range of potential paths to an atomic bomb all being researched at the same time with two paths leading to actual bombs. My point here being that developing an atomic bomb was in reality quite a lot easier than the Manhattan project, it's just that a sensible approach would have taken a lot longer. If anything what the game needs is some sort of simulation of the massive resource investment that was required to do everything at once. This is something that could be done by building in options relating to doing things in series rather than in parallel and adding idustrial cost to development as well as production. In the gamne industrial investment is only required for production.
Next point is that the in game effects of atomic bombs are somewhat greater than they should be. In reality the only thing that atomic bombs are really good at is destroying localised concentrations of resources whether they are civil or military. This makes them great for destroying single cities but against ,military targets you are quite limited. The effects you might expect were quite heavily researched post war with the conclusion that you can only significantly affect a single division of land forces and that fleets, like a carrier task force, are surprisingly survivable against this size of tactical warhead (which is what these first bombs were).
On the question of access to resources I would simply suggest there is minimal simulation of this (ie it's all in decisions and focus trees) because all of the major alliances in WW2 had adequate access to the necessary resources and hence simulating it doesn't actually achieve a great deal.
I would also agree with the point made earlier in the thread that the main morale affect on Japan was to persuade the emporrer that Japan should surrender. Any realistic morale impact of atomic bombs is going to be focused on the unknown threat of dropping many more. It is only with the advent of fusion weapons that nuclear attack become something that could win a war completely on its own.
One thing that isn't considered is the potential, with an atomic bomb, of aiming for extreme hard targets. The allies knew roughly where the fuhrer bunker was and roughly the location of other place where Hitler might be. They knew where the German high command was located. One of the effects never discussed for atomic weapons is the ability to take out invulnerable targets. This is something that could have ended the war in Europe 9-months earlier if A-bombs had been available a year earlier.
As it is we are having a fairly long-winded discussion about a fringe issue for HOI4 for the reason others have mentioned that they only appear at the end of the game. If, as often happens when I play, the war moves on into a second phase with the cold war immediately turning hot then a more realistic simulation makes sense but the main change needed is do something about the excessive effects. The main use I have for A-bombs is the destruction of enemy air power by attacking enemy airbases. This usually leads to my first wave of about 10 bombs destroying 10,000+ enemy aircraft.
