There was a lot of argument in SW about whether or not Lucas originally meant Vader to be Luke's father, and whether or not Uncle Owen's "That's what I'm afraid of" in ANH was about fear of Luke going bad. Now, I tend to come down on the side of it being intended, but ultimately, the argument doesn't even matter, because subsequent revelations would re-interpret the scene no matter what its original intention. I know that as a writer, I've been surprised by things that happen later in a story that cast earlier actions in a different light, but in terms of the story's arc, it's what ends up being the case that counts. Uncle Owen's line was foreboding in the context of "He might end up dead," but chilling in light of what we're to learn was actually the case about Luke's father. That's the case whether Lucas intended to follow that path during the initial writing or not, because what we later learn to be true was always true in the internal world of the fiction; we just didn't know it before (and the author may not have known it before). The new information revises the old understandings, and what is now so was always so.
Take a typical Law and Order kind of plot. There's a body, and the detectives start to investigate. A witness tells them that she thinks she saw "a guy in a red coat" running away. Further interviews give a few more details, and eventually, they come back to the first witness, and it turns out that she was expelled from a school whose varsity jackets are red. And, oh, the victim turns out to have been a legacy student there, and people had seen them together earlier. Ultimately, it works out that the killer was her partner and they were getting revenge on this privileged jerk who launched a complaint about her that got her expelled. It's certainly not the first assumption anyone made, but once it's revealed, it's not something that's newly become true; it's what the case was all along. We just hadn't discovered it yet.
To some extent, all stories are mysteries. We're dropped in in the middle of things, and we see things that we don't have explanations for. As the story goes on, we learn some back story (and don't learn other back story) that explains actions we initially see. We open HP up with Hagrid on Sirius's motorcycle and talking about what happened at Godric's Hollow. Later, we find out how he came by the bike, and that he believes he should have been suspicious because of the loan, and that Sirius was a very important figure that night. Did JKR know that when she wrote the opening scene? Most likely... but even if she didn't, it became the case when she wrote Prisoner of Azkaban. By the same token, Percy's behavior in CoS is only suspicious the first time through--once we've read the end and know that he's just nervous about revealing the fact that he has a girlfriend, his behavior makes a lot of sense. Was Sirius always the scion of a bigoted pure-blood family? Obviously, there were a lot of people pre-OotP who didn't think so. Well, now he was. Likewise, Snape was always a half-blood from a less-than-spiffy neighborhood, Tom Riddle's diary was a Horcrux, and Lily Evans was good at Potions. If JKR goes with "Snape had a great unrequited love for Lily" in book seven, I'll be annoyed by it, but... it will turn out to be what was always true, so reading back into the earlier books, it will be there.
Are there things that will be unsatisfactorily explained? Almost always. Why in the name of heaven did Sirius slash up the Fat Lady's portrait, or not go to either Remus or Dumbledore? Mad as a hatter only goes so far. Why did Uncle Owen let Luke keep his birth name? A matter to be addressed only by fic writers (be they pro or fan). Those things always seem to be left lying around. You can chalk them up to goofs or lazy writing, or you can come up with elaborate explanations, but either way, they don't change what we've learned about the underlying facts of the case.