For over 6 years people have been asking for a method on the bbPress forum to have a good hierarchical url structure.
The issue lies in the way bbPress treated a thread a topic and a reply as seperate post types.
tested against latest bbpress as of today 12/04/16
Download and install as a plugin. please test it first and back up things in case of problems.
provided as is with no warranty at all treat this as an alpha release.
Most of the work goes to https://github.com/korobochkin/bbpress-permalinks-with-id for the original steps and the rest is hopefully history.