The nosalises were added to the game because shooter games need generic enemies to shoot. They don't exist in the books, so the actual plot doesn't mention them.
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Also, blowing up the dark ones is canonically a bad idea. It's a representation of humanity’s tendency to react with irrational fear and violence against things we don't understand. If it seems foolish to you, congrats, you understand the point of the story.
In the book I don't believe they were nukes, just described as a pre-war missle silo. They fire 4 into the gardens, it's pretty clear in the games that the gardens and surrounding area are the home of the dark ones, they live really right on top of humanity. I haven't played last light tho so I'm not sure about anything else.
I think it was heavily implied to be nukes in the books but never explicitly stated.
The gardens were above a station that was abandoned though, so bombing it wouldn't do as much as if it was right over an active station.
Sequel expands but doesn't really change any of that stuff. To OP I would suggest playing the next one, it might answer some of the questions.
From what I understood, the gardens were, like, their headquarters. Bombing them would be their Achile's heel.
Indeed, as @FunderPants said, Metro Last Light should answer some of your questions :D