Parent-child-grandchild relationship for content or comments
I would go with option B, as having answers as content types allows you to add other features like the Flag module for up-votes.
The automatic and invisible reference linking can be done with the Entityreference prepopulate module, once there is a Drupal 8 version. You could also port it yourself or make an equivalent custom module. The older Node Reference URL Widget module would even add a link to your Question node on the Create Answer page with the appropriate URL adjustment for the reference.