I assume this is because comments get deleted by the mods.

Minor but important point: Moderators can remove comments, but not delete them -- only the person who created a comment (post, etc.) has delete privileges. Removed comments can be restored, and sometimes we restore removed comments if the OP (for example) edits in sources or does something similar. That's why they count in the comment count.

Now, deleted comments: If I understand it correctly, Reddit decrements the comment count for deleted comments if they do not have child comments, but otherwise does not.

As far as

Why can't the comment counters be decremented when this happens?

This is a Reddit-wide feature, not one that we have any control over as moderators.