At the end of Uncharted 4, Avery's ship explodes and burns to the water line, thanks to his traps, taking his treasures with it. However, the only other living person who has the faintest idea where the cavern might be is Nadine Ross, there's nothing preventing anyone from going back to the cavern (unlike previous lost cities, which were utterly destroyed), and Elena just happened to purchase a company that specializes in marine salvage. Given how well-to-do Nate and Elena are in the epilogue, it's entirely likely that Libertalia is the one lost city they were actually able to make some money off of. Even if the explosions and fires melted some or all of the currency, that's still got to be a couple of tons of gold lying in a secret cavern on a virtually uncharted island.
However the entire point of the story, and the treasure itself, is that those who seek it end up going mad and betraying those they seek it with. The more likely explanation is a simple one: Sam gave Elena some of the treasure before it all sank, giving her and Nathan enough to buy Jameson Marine and fund their new, completely legal, adventures from which they build their own fortune completely on their own. Sic Parvis Magna, indeed.
That, and nothing except the possibility of museums seizing the really valuable artifacts prevents Nate from calling in a legal, far safer and better supported expedition that could salvage what's left of the ship.. (leaving out how he found Libertalia) and giving both his and Elena's legitimate career a serious boost, to say nothing of tourists. At the end of the game, he probably was quite happy to hand Libertalia over to the authorities and wash his hands of the whole sordid business.
Also, unlike the first three games, there's nothing dangerous in Libertalia that could keep Nathan from revealing the existance of the ruins to the world after the adventure. He can never reveal the location of El Dorado to the public because the Descendants are still there and the virus is probably still salvagable, and both Shambala and Iram were demolished. But Libertalia is not only surprisingly intact, even with the damage of centuries of neglect, it's also an incredibly valuable trove of history for the Golden Age of Piracy, not to mention the remains of the Founders. It wouldnt be surprising if the place is a UNESCO World Heritage site by the time of the Epilogue.
One of Sam's lines, "Something on your mind, dear?" might be a reference to the same line in Fight Club. Which was released in 1999, the same year Sam ended up in prison.
Given that The chapter, "Hector Alcazar" is really just Nathan imagining the bogus story Sam is telling him, it makes perfect sense that Hector Alcazar is voiced by Robin Atkin Downes. Downes has voiced several antagonistic characters throughout the series, so it seems a perfect voice for Nate to associate with a villainous character.
There's a simple reason to why Sam is never mentioned in the previous games.
We are shown that Nate feels guilty after Evelyn dies, despite the fact that he couldn't have done anything to save her.
During Chapter 4, Nate refuses to look at the photograph of him and Sam as teens. Sam's "Death" traumatized Nathan so badly that even fifteen years later he cannot even look at him without it reminding him of the incident.
Thus, it could be possible that Nate feels so guilty about Sam's "death" that he physically cannot look at or talk about Sam without thinking about the moment he left his brother to die. As we are shown, he hadn't managed to tell even Elena, his wife, about Sam. This is also why others remain silent. They know better than to ruin Nate's day by bringing up Sam. When Sam showed up on his doorstep, he found out that he wasn't responsible for his brother's death, thus removing the mental barrier. However, this doesn't explain as to why Marlowe didn't exploit this in Uncharted 3.
Evelyn is basically an Expy of Lara Croft, and sends two significant figurative messages:
First, Evelyn is a subtle nod from Naughty Dog to the Tomb Raider franchise, from which Uncharted has drawn many of its influences from. Also, Evelyn giving Nate and Sam their mother's note book and regaling of the tale of Avery's treasure also serves as a figurative passing of the torch from Tomb Raider to Uncharted to carry on the action-adventure genre, which Uncharted did until the Tomb Raider franchise was recently rebooted.
Second, Evelyn acts as a cautionary tale to Nate. Like him, Evelyn was an avid adventurer who tried to settle down and have a family. However, she could never give up her adventuring, which eventually poisoned her family relationships, resulting in a nasty divorce, getting disowned by her own son, and living alone in an empty mansion with only her past collected treasures as company. She is what Nate could have become if he had decided to choose adventuring over Elena.
A subtle one. An early scene has Nate playing Crash Bandicoot, complaining about its lack of realism as Crash jumps over barriers and pits in an attempt to outrun various boulders. Later, in the booby-trapped caverns beneath Libertalia, Nate and Elena have to outrun impending doom (in the form of a corridor of exploding mummies), jumping over barriers, from the exact same perspective.
One of Libertalia's founders was none other than Guybrush Threepwood; there's a Running Gag that Nate has no idea who he is. This makes sense when you take the Crash Bandicoot scene into account; unlike Elena, Nate isn't that familiar with video games.
Nate wears his wedding ring all the time now. As our Fingore page will tell you, wearing a ring while climbing is a great way to get your finger degloved.
During the Italy chapter, Sam points to a 'radio tower' before Nathan corrects him that it's a cell tower. Sam is really out of touch with the world after all his time in prison.
There's a flashback to Nate and Sam breaking into a sprawling mansion to take back one of their mother's journals. The owner of the house - a sick, elderly woman named Evelyn - meets them and dies shortly after. Considering how alone she is, imagine if Nate and Sam hadn't decided to break into her house. In all likelihood, she would have died surrounded by nothing but her dusty treasures and weeks would have passed before anyone discovered her body.
Also, she wouldn't have gotten any closure or catharsis, and died with nothing but regrets. Sure, their visit may have been bad for her heart, but at least it wasn't a total loss.
Considering how strategically placed the exploding mummies are in Henry Avery's passageway, and how long it must have taken to construct, it's likely that the mummies are colonists who were conscripted into building them and then killed to keep it a secret. Which also lends credence to Elena's theory that Avery had always planned on stealing Libertalia's gold for himself.
Guybrush Threepwood was murdered alongside the other founders of Libertalia by Avery and Tew. That's where his adventures eventually got him.
In hindsight, it's incredibly lucky for Sam that Nate didn't know that Hector Alcazar, a famous drug lord, had been gunned down in a shootout — an event that would have doubtlessly made the news. Also, Nate never does a quick Google search on Alcazar or the Panama jail Sam was imprisoned in; both things that would have quickly exposed Sam's lies.
Nate actually lampshades this some time after Elena rescues him.
It can be argued that Sam knew this and why he did it. He figured Nate would be so overjoyed seeing his long-dead brother alive again that it would never occur to him Sam was playing some line.
Another genius idea is how it's been shown Sam, having been in a South American jail since 1999, is pretty out of date with the modern world (he mistakes a cell phone tower for a radio one). Thus, Sam still thinks people read newspapers regularly and Alcazar's death wouldn't have been as big a story for Nate in the U.S. The idea of people constantly checking the Internet for news and finding things easily wouldn't be crossing Sam's mind. Thus, he really has no idea how flimsy his story is and lucky Nate never bothered to check on it.