Harry's suggesting that Voldemort's tactics involve not just hate but an incredible degree of cynicism.
Both "Make Bella love you despairingly, on purpose" and "Mess with Hermione's brain intimately over a long period of time" reflect a person who can get to know people closely and accurately and yet not care about them at all.
A lot of evil comes from people doing bad things to people they don't bother to think about in the first place. Voldemort clearly took the trouble to get to know Bellatrix and (somewhat) Hermione rather well - solely for the purposes of undermining them.
Some police trained as hostage-situation snipers find they can't actually pull the trigger on real criminals, because they watch them so long and so closely they empathize with them. Draco Malfoy, in the fic, was coming to empathize with Hermione Granger.
Harry is observing that Voldemort seems to be immune to natural empathy, and that creeps him out.
(Agree that Harry having "Voldemort plot detection powers" as a general rule would be bizarre.)
Voldemort isn't the only empty one.
Quirell "cannot say that I bothered keeping count" of "how many different people" he is. Surely he has an empty persona. It's useful.
EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author's Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven, eight, nine, ten.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: