I haven't deleted anything, and looking at them now I can't think of any which are missing. Disqus glitch maybe?

Probably right, sorry for jumping to conclusions too hastily (a common antipattern on the ol' internets). Certainly if someone deleted a parent comment, there's several design decisions for comment services on how to handle child threads. One would hope that if a parent comment were deleted, it would leave a placeholder like HN, but it's doubtful that it's only design branch taken.