Ianto's feelings about Jack are complicated. For him they're very deep, but at the same time he knows Jack doesn't feel the same way about him (partially because he has eyes and can see the way Jack behaves around everyone else, and partially because he has a deep-seated belief that he isn't worthy of someone having those sorts of feelings about him). Being away from Jack only cements those negative feelings (because he doesn't have anything to reinforce the positive ones), so it's just sort of another thing in a long line of things that are weighing him down. Ianto isn't happy here, and though he's had moments where he's felt better, he's generally very depressed.

If Jack came to Darrow, however, I think Ianto would throw himself into Jack's arms and never let go again.

At the moment Will is in a weird place as far as Hannibal is concerned. They have an unspoken understanding, but Will's falling in love with a woman for the first time in his life, and he's afraid of what it will do to the dynamic. He's not worried about Molly (because she's more than capable of defending herself), but he is worried about himself (because Hannibal has so many ways he could take Will down). right now he's able to sort of avoid dealing with it (because he and Hannibal haven't been around each other much), but he knows eventually he's going to have to start watching his back.