Sam being in trouble is straight up obvious. Nothing implied there. You only have to play through chapter 4 once to realise that Drake wants to go out on adventures again. Not implied. Obvious. Feeling guilty because of Sam... less obvious but not implied. The chapter of them being younger, and chapter 4 pretty much tells you what you need to know about his relationship with his brother. Trying to look at Sams picture is a memory that clearly is too much for Nate to deal with.
So I wouldn't say any of these plots are implied.
And those other more painful scenarios: did any of those involve the death of someone Nate cared for? and from his past? Its not the same thing. As for the UC3 thing, well UC4 tells you that when Nate and Sam were younger that Sam was in and out of jail a lot. There we go. Sure the thing with Marlowe is strange but Sam is believed dead at this point. What exactly does she gain from bringing up Sam at all at that point? But sure, i can see what you mean here.
And Sam being hateful of Nate be incredibly cliched in itself (oh you abandoned me and now I hate you because you never came to visit).
Anyhow, I think complaining that Nate wouldn't have kept Sam a secret from Elena is a pretty weak point to make. There are so many influential decisions we make throughout our lives that change how each of us think, react and reflect on any given situation we are in. Nate not telling Elena is not some unexpected human decision. Its a painful memory... and its pretty clear that he likes to keep his past a secret from everyone. That is a pretty defining element of the narrative in UC4: the secrets we keep and how perhaps we shouldn't hide things from the people we love most. Nate does this to Elena. Its hurts her and their relationship. Sam does it to Nate. It hurts him and their relationship. Nate and Elena decide not to it to their child.
You do know that Nate in the attic and the way he looks at the frame on the wall is where writers are telling viewers that nate misses the adventure its not left on viewers interpretation. which was not at all obvious when he was diving and refuses Malaysia job.
Sam being in trouble is straight up obvious - that was implied from the first trailer that was the plot line of all the trailers. the only obvious thing was sam had a secret, what it is that was the hook of the story
What exactly does she gain from bringing up Sam at all at that point? - for the same reason she brought up his mothers suicide, which in my books and should be more painful considering that is one of the sub plots of UC4 searching for her journal.
and also about painful deaths, Nate though he lost elena at the end of UC2, and at the end of UC3 it was sully, sure they didn't die but psychological ramification is as equal as losing a loved one. So nate knows how to handle that emotion, just assuming its too painful for him is a weak character arc.
In the end there was no point in hiding about Sam from elena considering everyone else knew about him. Sully and chloe.. especially sully, he could have told elena about sam, without involving Nate if it was as u said "too painful" just for a heads up, Like hey listen nate had a brother who died in a prison break out and its painful for him to remember, so this is just for you info. Also isn't sharing about your family member details one of the important element in building a strong relationship.
the only good part about UC4 was how neil and bruce handled unspoken conflict between elena and Nate in the middle to end part, but i think that has more to do with Nolan and emily's performance. The reason why that conflict happened was weak.