Hello Jeremy,
Yes, I am aware of this. Orphaned posts are disconnected from the main thread, this is one of the down sides to allowing users to delete their own posts. The logic is, responses to posts which have been deleted are orphaned because the lineage of responses are no longer connected to the original post and become out of context. However, these individual children posts are still able to be accessed directly, as they may still be pertinent by themselves. Allowing users to delete their own posts, and deactivating posts within threads creates this problem.
I see two possible changes which may help with the confusion, but have negative aspects as well:
1) Automatically deactivate all child posts off of a post which has been deleted or deactivated. This cleans up the issue with orphan posts still showing up in certain views, but may remove helpful content.
2) Remap all orphaned posts onto the ancestor thread. This keeps all posts in the thread even after being orphaned, but the conversation then may be confusing, as posts have been removed from the middle.
The mechanism which currently exists, and has existed for many years, is in place because of the drawbacks above.
Abraham