If I understand your question right, you want to compare two different things (concepts, etc.), but the descriptors that you use for the things are not analogous to each other.
That can definitely sound a little weird:
"The enormous paw prints in the mud were mistaken for a tiger."
"The delightful aromas of frying onions and roasting chicken could easily be mistaken for our own kitchen back home."
If this parallelism problem is what you are asking about, those two sentences above could definitely use some help.
But the examples you give,
The explosions were mistaken for Russian nukes.
The looming clouds were mistaken for Russian nukes.
both sound reasonably natural and idiomatic to me. I don't think most people would have a problem with the wording, especially since "nuke" is just short for "nuclear", and it could just as easily stand for "nuclear explosion". It can even be a verb.
But it sounds like it bothers you to say that a cloud (atmospheric condition), or an explosion (big boom), could be mistaken for a bomb (military device).
The reworked sentences you propose:
The explosions were mistaken for the explosions of Russian nukes.
The looming clouds were mistaken for the fallout of Russian nukes.
don't really sound awkward or nonsensical either (to me, anyway). But if you want the two halves of your statements to line up perfectly (apples-to-apples & oranges-to-oranges), you have three variables to work with:
A) first item:
The origin of the mushroom clouds was mistaken for Russian nukes.
The animal that made the enormous paw prints was mistaken for a tiger.
B) second item:
The looming clouds were mistaken for the result of a Russian nuclear
The enormous paw prints in the mud were mistaken for those of a tiger.
C) the relationship between the two items:
The explosions were initially thought to be from Russian nukes.
The enormous paw prints in the mud were wrongly attributed to a tiger.