I don't have a problem persay with the portrayal of Jonah/Elias having problems with empathy or emotions or human connections (beyond my generalized issue that any time anyone behaves meanly they're immediately stamped as low/no empathy which. is annoying, but that's a conversation for another day), but I don't think I agree with it entirely, either.
He doesn't behave the way he does with the Archives crew or with Jon because he's incapable of understanding or perceiving their feelings, or of identifying with them. On the contrary, he's really very emotionally perceptive with the people around him, and engages fairly openly (for his personal given value) with them right up until like. mid-season 4? He's playing mind games left right and center, of course, but again that isn't because he doesn't understand that it might upset people to do that. I don't even really think it's because he doesn't care, at least not exactly.
We are following this unraveling existential fear nightmare with a group of people to whom it is new. And upon first listen, it was also new to us! Do you know who it 100% was not new to in any capacity? Elias. And in fact, it has not been new to Elias in like. 200 years.
The Archives crew and all of us listening in are babies in a scary new world, knocking into things and fumbling around on wobbly legs trying to identify what's safe and what isn't. It's not that Elias is incapable of understanding or identifying or even empathizing with how upset everyone is, it's that by comparison these are children who have skinned their knees at the playground, and he is an ostensibly 200+ year old adult who knows that, if they just get up and keep playing and learn more about the world, they're going to be fine (for his personal given value. 'you're going to like it here, in the world we've made' etc etc).
In fact, the few times that Jon directly goes to Elias for explanation or comfort or to confide his concerns, Elias actually does give him those things. He's literally, very VERY literally, been exactly in Jon's position, except when he was there it was totally without the benefit of guidance or context. I don't think his conversation about "even when you had the entire archive at your disposal you only made it through a couple a week, why do you think that is?" was insincere or unhelpful. Wanting all the answers and for everything to make sense immediately is understandable but not possible. Not for the version of Jon demanding those answers. Not for Jonah, when he was careening through all of this on his own.
This is a man who started off passionate and curious and brilliant, who poured himself into understanding and prevention of the damage done by the Fears, and it's also a man who watched everyone else in his little cohort die, who outlived them all, who watched the world changed and gained the understanding he sought and found that desperate death grip on fighting the good fight to be futile.
It isn't that he doesn't have emotions or feel empathy. It's that he has a completely different world view, different conclusions, different ends, and has had time enough to let go of the reflex to wring his hands about it all. Has that made him very nice, particularly? No lmfao. But I feel like it flattens some of the nuance of his character to be like "oh he just doesn't get people or feel human emotions and that's why he acts that way."