The official novelisation gives us some insight into Luke's thought process. He doesn't have an inkling that Vader...
is his father
... before Vader tells him, but when he examines his feelings, he does indeed feel that it's likely to be the truth.
“Search your feelings,” Vader said, sounding like an evil version of
Yoda, “you know it to be true.”
Then Vader turned off the blade of his lightsaber and extended a
steady and inviting hand.
Bewildered and horror-stricken at Vader’s words, Luke shouted, “No!
No!”
Vader continued persuasively. “Luke, you can destroy the Emperor. He
has foreseen this. It is your destiny. Join me and together we can
rule the galaxy as father and son. Come with me. It is the only way.”
Luke’s mind whirled with those words. Everything was finally beginning
to coalesce in his brain. Or was it? He wondered if Vader were telling
him the truth—if the training of Yoda, the teaching of saintly old
Ben, his own strivings for good and his abhorrence of evil, if
everything he had fought for were no more than a lie.
He didn’t want to believe Vader, tried convincing himself that it was
Vader who lied to him—but somehow he could feel the truth in the Dark
Lord’s words. But, if Darth Vader did speak the truth, why, he
wondered, had Ben Kenobi lied to him? Why? His mind screamed louder
than any wind the Dark Lord could ever summon against him.
The answers no longer seemed to matter.
His Father.
With the calmness that Ben himself and Yoda, the Jedi Master, had
taught him, Luke Skywalker made, perhaps, what might be his final
decision of all. “Never,” Luke shouted as he stepped out into the
empty abyss beneath him. For all its unperceived depth, Luke might
have been falling to another galaxy.
