out of curiosity why should the attacking nation get a malus for using one? today i could see it with the prevalent information on the effects of a nuclear detonation (ie radiation sickness) at the time it was seen as a means to an end. in which the means justify the ends it was total war with victory at any cost
As usual, I would seperate gameplay and realism:
gameplay: Include a harm for the nuking side to have a counterweight against nuke spamming which seems very much possible, if one reactor means 1 bomb per year (see last MP-WWW). Building 24 reactors seems doable for e.g. USA which seems to result in a kind of ridiculous nuke-a-palooza.
realism: Immediately after the first tests, scientists knew exactly what they did, see Oppenheimer's famous quote from the baghavid-gita. And while popular reaction to the use of nukes against Japan may have been positive (I am not so sure about the unanimous character of it, though), subsequent nuking over months or years (as we might very well see in game) would certainly have lead to opposition, domestic and international. At least I believe so.
So the returns may not be relevant after two or three bombs, but after 20, they should be painful, at least noticable, in a way to make the dropping party consider.
Alternatively, one might consider to make nukes cost IC (which would be issue of balancing, of course). This would serve kind of the same Goal, to limit the use. At the moment, they seem to be free once the reactors are built.
edit: Additionally, we should Keep in mind that the representation of nukes in anything but realistic. For example, in WW2, noone would have evernuked the capital of an enemy nation. Yet this seems to be the first thing to do in HoI4 when considering NU-Impact. So we should look at it as a game-mechanism rather than a representation of reality.