First of all , I agree that the best solution is to have nuking afecting everything including zombies and neutral lemmings , that gets my vote ! But please , don't remove nuke solutions !
The argument that originally meant to be just a way to end the level ,I don't consider it strong enough! If we use the same logic , release rate also in many cases doesn't used nowadays as originally intended. In the Amiga version it's just meant to be a fast forward option because the Amiga version didn't feature a fast forward option like the modern players have. (onml with levels like havoc 10 released later).
And the most important is that some very creative, unique and impressive levels have been relased that use very smart nuke solutions. Some of these are amongst my favourites ever, and one of these is so iconic, that it has currently 4 different versions. So now it will be playable on Lemmix and not on the new formats Neolemmix? It would be a shame imo if we would lose levels like these.
So in conclusion, make the nuke affect everything, keep the nuke solutions, and also keep the countdown counter on nuking, because it makes levels as the ones I mention playable, and also it adds a sense of tension before the nuking.