This works in Nick's favor: Amy likely wouldn't get away with what she did for long....she forgot to burn the car she abandoned....in the parking lot of a Las Vegas casino. As Cracked points out, in Movie Land, objects disappear the moment they're no longer needed for the story. In real life, cars that are abandoned in public parking lots will quickly attract attention from the police. This would happen pretty quickly given the scenario here. The police will run the plates, the VIN number, everything, to track down the original owner, who will say that they sold it to some woman via the Internet. This person has probably seen Amy's face on TV by now — if not during the initial coverage of her disappearance, then surely during the media circus her spectacular return caused. The moment he realizes who he was selling the car to, he'll surely come forward. And the moment the police realize that Amy was at the casino, her whole web of lies will collapse instantly. Why? Because after dumping the car, Amy meets Desi inside the casino, and casinos have almost 100% surveillance coverage to crack down on cheaters, so unless the most inept detectives ever are assigned to the case, they'll eventually find surveillance footage of Amy sitting down and getting all chummy with her so-called "abductor."
There are also the cameras in Desi's house, which would have taped everything, to consider. And there were loads in the house.
We may assume that Amy asked Desi to dispose of her car, so that line of evidence was gone. In the novel, they dump the car and Purel every inch of it. The casino tapes would still exist, but no one would know to go looking for them. And she may have messed with the lake house security system to delete whatever particular footage didn't fit her story.
Except then that will create inexplicable blank spots in the time stamps, which would only serve to draw more suspicion on her, since with Desi dead, she was the only one who could have possibly messed with the footage, and the only one with the motive to do so.
Small detail, but most systems like the one Desi has don't store their footage for very long. It's a very similar system to the one at my former workplace, which only stores everything for several days. The movie takes place in 2012, when cloud-based security systems were still very expensive and niche, even for a man of Desi's considerable means (after all, it's just a lakehouse, not a multimillion dollar business).
All that said, yes, there was still plenty that could technically damn Amy, but it seems that the stupidity exists in-universe. For example, Amy claims in the novel that she miscarried too early to require a DNC. At somewhere between six and 10 weeks pregnant, a doctor wouldn't simply know by looking or talking to her that she wouldn't require a DNC. She underwent a pelvic exam to confirm the signs of rape, but there was positively no sign of a pregnancy or miscarriage which would be physically impossible. One of the first things they would have done is check for signs of a miscarriage, since an untreated miscarriage can lead to serious infections. She also claims that her pregnancy was confirmed as part of her "legal medical record" and gets around using a blood test by claiming a fear of blood. However, at six weeks, it would take more than urine to "legally" confirm pregnancy a dating ultrasound is usually done. And although Amy had the forethought to roll around in Desi's trunk and leave her long hairs in there, she had no way to account for possible alibis of Desi. The amount of blood she "lost," according to various doctors and medical experts who have watched the film, was enough to kill her, which the novel and movie merely brush off as an "ow" moment. No one thinks to question delivery men about the items delivered to the shed, and we're supposed to believe that Amy transported a massive television in there by herself. Amy's holding of the Punch and Judy toy is never explained and she merely feigns discomfort to get out of questioning. The investigation is essentially called off based on testimony alone. So while yes, Amy could have been "found out," that's only if the police force in-universe functioned like a real police force. Which it doesn't.
Amy has a massive Misaimed Fandom, with people thinking of her as some sort of feminist heroine (never mind that Amy makes false rape accusations, is a total hypocrite, and clearly looks down on women herself), and that her framing of Nick was not only understandable, but justified. Even though she's the villain, she still has plenty of people on her side, viewing her as a victim and Nick as the real monster. So in other words... her fake diary worked perfectly.
That kid is going to have Amy as a mother, and Amy has already threatened the kid's life as a bargaining chip before they're born. That alone is Nightmare Fuel. Let's pray Amy kicks the bucket before that kid can grow up around her for too long, the sooner the better...
Forget Amy. How about Amy AND Nick?
In the film, Amy says during the interview near that end that Desi sodomized her as 'punishment'. So...did she use a wine bottle for that, too? SQUICK!
It's very common in Real Life for children with abusive parents to later end up in abusive relationships. This happens to Nick to a T.
...and is highly likely to happen to their child, too.