1)
The conjunction ところで is usually written in hiragana.
2)
コーヒー is not the main topic of the whole sentence. The question is asking about the existence of 人, not コーヒー, i.e., the core of the sentence is 人はいませんか, and not コーヒーはいませんか. コーヒー is the topic of the quotation.
3)
Even if it's an affirmative question ところで、コーヒーは体に悪いと思っている人はいますか。, は is also used. Remember that the focus is put before は and after が, thus, "whether there is anyone ~ or not" is what the questioner is asking about in this case.
The reason why は is often used in a negative sentence is because it usually connotes that other thing is affirmative, e.g., "French people don't exist, (but other people exist)". Thus, you can think that this は is the contrastive marker.