During copyright registration will they ask whether we had the permission to take some photos if it appears that permission might have been needed to even take the photo? Or they only care about who took the photo and if there was no existing copyright, and as long as we take the photo, it is ok?
You don't mention where you're thinking of registering copyright. There might be some country where there is an exception, but in general the copyright office doesn't go into details such as this. They won't even investigate whether the registered work violates someone else's copyright.
If the work violates someone's right, whether it is a right not to be photographed without permission or copyright or something else, tbe person whose rights are violated can sue you or seek whatever remedy the law provides through whatever process the law provides. This is true whether the work in question is registered or not. So the copyright office just registers the work.
If you have the copyright on a photo, that means nobody else has the right to copy it without your permission. But apart from that, nobody, including you, is allowed to copy the photo if there is some other reason why you are not allowed to copy it. Like having no permission by the people in the photo, or something illegal about the content of the photo.
Copyright registration is not affected by this. It's just that you can at the same time be the copyright holder, and be not allowed to copy it.