Would it be difficult to arrange matters so that the Whatlinkshere page showed indirect links through a transcluded template in similar fashion to those through a REDIRECT page?
The next question would be whether it might be possible to add a twist-down button like on "enhanced recent changes" so that these "sub-trees" could be hidden, which is obviously doable, but since the equivalent suggestion for TOCs has been sitting in the queue for lo-so-many-yonks I wouldn't want to be holding my breath for it.