Basically it's a matter of grammar rather than nuance.
As you may know, 「は」 in 「ではない」 is (semantically almost bleached out but still functioning) topic marker in the theme-rheme structure of Japanese.
In other words, it delimits theme and rheme parts of a clause.
And one clause may only contain up to one theme and rheme respectively.
Then, what happens if you use two は at once in a sentence?
You may feel a sense of dissonance because:
- 核兵器は [ [ 使用するべきで ] はない ]
- [ [ 核兵器 ] は使用するべきで ] はない
It has two possible breakdowns so you can't decide which is the main theme of the sentence.
(Note that some people don't feel anything wrong because they conceive ではない to be a monolithic chunk.)
Thus carefully written sentences often omit the は in ではない in order to avoid confusing readers by any chance.
Of course, in the colloquial language, じゃない has taken over them so that the difference between でない and ではない is neutralized.