Are some of the challenges/treasures possible to miss forever?

No, none of the challenges and treasures can be missed forever. The developers have been careful on not putting any of this kind of content in the "one time only" zones. They've done a great work, instead, in hiding in plain sight your goals. As you should already know, all of the "Challenge" content doesn't show on the map, even with every ability unlocked, so you'll have to explore every inch of the map to find what you're looking for.

About the mines, you should search for them in the sea mostly, possibly behind rocks and eventually only reachable with your weapons (zooming can help).

You should be able to reach the document too, since it should be in the part of the Endurance that

didn't sink after the explosion.

I have 100% and every challenge is still reachable after game completion.

The sea mines are one of the toughest, mainly because a couple are out to sea far enough that they don't glow when you use survival vision. They're only visible during the low part of each wave.

The section of Shipwreck Beach that you jump across cable cars to get to can't be reached again, but it has no challenges. They're all in the Research Base.

After the quest in the Endurance you can still zip line back to the rear of the boat by the same route you used before.