do you think benjen knew the truth about jon? or at least suspected it?
I like to think he suspected it, possibly even knew with certainty without Ned telling him. There’s a theory floating around that Benjen joined the Night’s Watch out of guilt because he knew of Lyanna’s plans to run away, so maybe when he saw Jon he just *knew*.
Benjen is particularly warm toward Jon, even joining him at the low table during the King’s feast in Winterfell to talk to him and tease him. That particular interaction doesn’t end well because Jon’s drunk and angry, but Benjen does say this:
“You might, if you knew what it meant,” Benjen said. “If you knew what the oath would cost you, you might be less eager to pay the price, son.”
Jon felt anger rise inside him. “I’m not your son!”
Benjen Stark stood up. “More’s the pity.” He put a hand on Jon’s shoulder. “Come back to me after you’ve fathered a few bastards of your own, and we’ll see how you feel.”
Jon even becomes sullen that Benjen stopped being as friendly with him when they went to the Wall, because Benjen is trying to make a point that he’s just another brother at the Wall and would not get special treatment from him:
Even his uncle had abandoned him in this cold place at the end of the world. Up here, the genial Benjen Stark he had known became a different person. He was First Ranger, and he spent his days and nights with Lord Commander Mormont and Maester Aemon and the other high officers, while Jon was given over to the less than tender charge of Ser Alliser Thorne.
Three days after their arrival, Jon had heard that Benjen Stark was to lead a half-dozen men on a ranging into the haunted forest. That night he sought out his uncle in the great timbered common hall and pleaded to go with him. Benjen refused him curtly. “This is not Winterfell,” he told him as he cut his meat with fork and dagger. “On the Wall, a man gets only what he earns. You’re no ranger, Jon, only a green boy with the smell of summer still on you.”
Stupidly, Jon argued. “I’ll be fifteen on my name day,” he said. “Almost a man grown.”
Benjen Stark frowned. “A boy you are, and a boy you’ll remain until Ser Alliser says you are fit to be a man of the Night’s Watch. If you thought your Stark blood would win you easy favors, you were wrong. We put aside our old families when we swear our vows. Your father will always have a place in my heart, but these are my brothers now.” He gestured with his dagger at the men around them, all the hard cold men in black.
Jon rose at dawn the next day to watch his uncle leave. One of his rangers, a big ugly man, sang a bawdy song as he saddled his garron, his breath steaming in the cold morning air. Ben Stark smiled at that, but he had no smile for his nephew. “How often must I tell you no, Jon? We’ll speak when I return.”
Jon expresses a great amount of anger over his uncle’s treatment of him, which seems to indicate that Jon is very much unused to Benjen refusing him or being anything less than warm toward him. His anger reaches a boiling point pretty quickly too:
“I don’t care,” Jon said. “I don’t care about them and I don’t care about you or Thorne or Benjen Stark or any of it. I hate it here. It’s too … it’s cold.”
When Benjen goes missing, it affects Jon rather greatly throughout AGoT:
Jon remembered the wish he’d wished in his anger, the vision of Benjen Stark dead in the snow, and he looked away quickly. The dwarf had a way of sensing things, and Jon did not want him to see the guilt in his eyes. “He said he’d be back by my name day,” he admitted. His name day had come and gone, unremarked, a fortnight past.
For a moment Jon was too frightened to move. Why would the Lord Commander want to see him? They had heard something about Benjen, he thought wildly, he was dead, the vision had come true. “Is it my uncle?” he blurted. “Is he returned safe?”
The grey walls of Winterfell might still haunt his dreams, but Castle Black was his life now, and his brothers were Sam and Grenn and Halder and Pyp and the other cast-outs who wore the black of the Night’s Watch.
“My uncle spoke truly,” he whispered to Ghost. He wondered if he would ever see Benjen Stark again, to tell him.
“Very well, truly,” the fat boy lied. “I am so happy for you all.” His round face quivered as he forced a smile. “You will be First Ranger someday, just as your uncle was.”
“Is,” Jon corrected. He would not accept that Benjen Stark was dead.
“Benjen Stark is still First Ranger,” Jon Snow told him, toying with his bowl of blueberries. The rest might have given up all hope of his uncle’s safe return, but not him.
In ACoK Jon still thinks of his uncle, and even mentions him to Ygritte:
“Do you know anything of my uncle, Benjen Stark?”
Ygritte ignored him. Stonesnake laughed. “If she spits out her tongue, don’t say I didn’t warn you.”
In Jon’s crypt dream in ASoS, he calls to his uncle for help:
He dreamt he was back in Winterfell, limping past the stone kings on their thrones. Their grey granite eyes turned to follow him as he passed, and their grey granite fingers tightened on the hilts of the rusted swords upon their laps. You are no Stark, he could hear them mutter, in heavy granite voices. There is no place for you here. Go away. He walked deeper into the darkness. “Father?” he called. “Bran? Rickon?” No one answered. A chill wind was blowing on his neck. “Uncle?” he called. “Uncle Benjen? Father? Please, Father, help me.” Up above he heard drums. They are feasting in the Great Hall, but I am not welcome there. I am no Stark, and this is not my place. His crutch slipped and he fell to his knees. The crypts were growing darker. A light has gone out somewhere. “Ygritte?” he whispered. “Forgive me. Please.” But it was only a direwolf, grey and ghastly, spotted with blood, his golden eyes shining sadly through the dark …
All of this to establish that a relationship did exist between Jon and Benjen, and overall it seemed a rather warm one. It’s just as well that Benjen would behave warmly toward any Stark bastard, but seeing as Benjen and Lyanna had been close in age, that they likely spent more time together than Benjen would have with his other siblings, and that they were partners in crime at Harrenhal may indicate that he feels close to Jon because of Lyanna.