So, thinking about it more, the issue is in the description.
"I use my bonus action to put manacles on him"
Rolls are had and DM narrates success. "He's all tied up and can't swing his sword. He's at disadvantage to attack"
I'd require more description: "How will you put on the manacles? He's looking at you as you approach. Are you putting them on his wrists or his ankles? Are you trying to tie his limbs together or are you trying to tie him to an obstacle or another person?"
From there, it seems easier to adjudicate. I come to this conclusion trying to imagine what my character would do to defend himself against the rogue if the rogue was dominated or something. if I keep my arms apart instead in a sword/sheild combo instead of wielding a sword in two hands, he can't lock my arms together. If I keep my stance wide, he can't lock my legs together. To do so, he'd need to physically move my limbs together which would require athletics (which I'm trained in) instead of Slight of Hand.
Essentially, 'I know the trick' so I can deny him the use of his apex skill which relies on distraction and deception.
So, given that train of thought, in combat, for a rogue (or anyone) to slip on manacles as an action, with slight of hand, they'd need to have surprise: the target must be distracted and not expecting to be manacled(probably requiring a stealth check, at the least). The action (what body part do you manacle) must make sense for the stance of the attacker also. I'd say that trying to manacle to hands together to be almost impossible. But you might get one hand. Or you might even be able to manacle two people together.
Essentially, each situation might be adjudicated differently instead of a general 'Slight of Hand vs opposing skill'.
My overall impression is it might take multiple actions to 'lock' someone down.