I think it would be unfair to say that Quran doesn’t address atheism, agnosticism & similar way of thinking . The more appropriate statement would be that Quran has vehemently condemned Shirk and has given arguments to counter an atheist mind and to help an agnostic mind in it’s search for the truth. A significant portion of Quran contains arguments ranging from intuitive, intellectual and historical domains. And then there is empirical evidence in the form of results of ittemam-e-hujjat that happened in the land of Arab. I think it’s only fair that a thinking mind or questioning mind should not be condemned vehemently, rather it should be given arguments to use it’s thinking faculty in order to reach an educated conclusion. On the other hand, Shirk should be condemned vehemently as there is no philosophical basis for shirk.
As far as Surah kahf verses 32-46 are concerned, I think yes, it does fall in a category of Shirk. There is a kind of Shirk where you associate someone else a partner in attributes and creation of God. & sometimes a person can fall into a delusion where he considers himself God. A person can be blinded by success, fame and too much affluence where he starts associating everything solely with his efforts and with every success, his pride and arrogance goes one step further. This, I think is a more dangerous form of Shirk because a person gets so intoxicated with the world around him at times and he thinks that this whole world revolves around him only; a time when all Dawah is useless on him, all reminders of the truth prove futile. I personally have seen such people and their mental state is no different than Pharaoh as mentioned in Quran. May Allah save us from such delusions and from the intoxication of this worldly venom. Ameen! But, in my opinion, it would be unfair to class everyone in today’s life in this category. Those who pray five times a day, are constantly reminded of the truth and it helps them to not let this blind of worldly successes & fame fall before their eyes. If there’s venom, then God has prescribed it’s antidote as well.
Since I haven’t read Islahi Sahab’s book which you mentioned, so I can’t comment on that. But I can say one thing, according to me, self-accountability is definitely a continuous process, and everyday should be an attempt to be a better person and a better Muslim than the previous day.