I have not read the original Harry Potter series. I first learned that Quirrell was Voldemort when, after finishing the 49 chapters of MoR out at that point, I followed a link from LW to the collected author's notes and read those.
I think that for those who have not read the source material (though there may not be many of us), it is basically impossible to intuit that Quirrell is Voldemort from the body of the fanfic so far.
That said, I don't feel like I missed out in any way and don't see why it necessarily needs to be any more explicit until the inevitable big reveal.
Edit: I just remembered that, as you can see, my prior comment on this post was written after I read chapter 49 but before I learned that Quirrell == Voldemort.
Eliezer planted lots of clues about many facts that are never explicitly revealed, in such a way that noticing correct hypotheses is sufficient to confirm them upon observing enough of those little clues. Now, for some facts, it could be difficult to even locate them, but Quirrell=Voldemort seems to be a good hypothesis to entertain, even if it's not apparently confirmed from any single passage, and it does get lots of evidence if you know to look for it.
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.