Ianto's never asked him outright, but Jack knows he wonders. He hints about it, in his own subtle way, asking if he thinks Beth is gone completely and there's only the Sleeper left (no), asking if he thinks Beth can't be trusted (not entirely), and, afterwards, asking Jack if he's alright (about Beth, yes).
Ianto never comes right out and asks Jack why he treated Beth so badly. Gwen does, and he pawns her off with excuses about not being able to trust that there wasn't a hidden layer of programming (he wouldn't have been able to do that if Ianto hadn't thought of it first).
Ianto trusts Jack to tell him when he's ready. Jack trusts Ianto not to push. They fit together remarkably well that way (physically they fit together well, too, but that's not so remarkable – for Jack).
Later than evening, as they're sharing a cup of coffee (one cup; they don't even need the kisses in between sips to have romance), Jack takes a deep breath and prepares to not-lie to his lover yet again. "Beth…when she…turned on everyone so suddenly… I…" This isn't nearly as easy as he'd hoped it would be (but then, nothing is when it comes to Ianto).
Ianto places a steadying hand on his, and Jack raises his eyes from the floor to focus on the middle of Ianto's forehead. He can't meet Ianto's eyes when he says this, but it will look to Ianto as if he is. "It brought back some bad memories…that's all." And Jack swallows down his guilt and leans in to bury his face in Ianto's neck, letting his self-hate melt mostly away in his lover's comforting embrace.
It's the truth, of a sort. But Jack loves Ianto, and he does his best not to hurt him (when he isn't caught up so much in his own pain or the job that he remembers to).
He's forgiven the Doctor, but he's not sure he can trust him, personally, again. After a year of being tortured, Jack finds it hard to trust anybody. But he will force himself to trust Ianto, if he has to, because he cannot imagine making it through this life sane without him.
So Jack won't tell Ianto how this whole thing with the sleeper agents reminded him so very sharply of when he had discovered Ianto's own betrayal, with Lisa.