Some comic canon here.
It's not hard to keep secrets. When you're the director of a highly-classified, quasi-militaristic intelligence agency, secrets aren't just things whispered about in corners, they're a way of life.
So covering up things becomes far too easy. Especially when it's personal.
Like pain. There's something about it – a constant dull ache interspersed with sharp, stabbing red-hot irons lancing through his head – that makes Nick Fury not want to get up in the morning sometimes. Some days it's easier to just pull the covers over his head and pretend that the outside world doesn't exist. Then the phone rings or his alarm goes off, responsibility comes crashing back in, and he blindly gropes for the bottle of painkillers he keeps next to his bed.
He's worked hard to cover it all up, but there are days when he emerges from his quarters, mentally daring anybody to say anything to him until the drugs have had a chance to kick in. Those days, Hill just gives him a look and Fury knows that something – the set of his shoulders, that muscle that occasionally twitches in his jaw – gave him away. So he just looks back at her with a small nod and a quiet "Good morning, Agent Hill," and watches as she turns around and continues to make sure that everything runs smoothly for another hour, until he feels that he won't feed into the desire to share the pain with anybody who talks with him. Or even looks at him funny, or breathes too loudly.
The doctors are the only ones who truly know what goes on in his head with the pain, and that's only because Fury ends up in their clutches once or twice a year. Any shrapnel that's still present has been there for decades now, slowly working its way around his eyeball, and that's what they say causes all of the problems. It's almost become a game by now: the doctors offer to simply remove his eye since he doesn't use the miniscule vision left in it anyways, and he harangues them into just giving him a year's supply of Tylenol and ibuprofen because his eyepatch works just fine, and he's not going under the knife unless it's a life-or-death situation. They compromise with numbing eye drops that he'll use when the pain hits the point where he's almost – almost – agreeing to the surgery.
But he'll be damned before he lets them cut anything out of his body that he wasn't born with, so Fury just hides it all. The pain always dulls, always retreats to the very back of his awareness to the point where he's able to ignore it and go about keeping the world safe.
He's a spy. He's had practice at hiding everything, after all, even from himself.
