Kensi pulls Dom aside on Callen's first day back to warn him. Yes, everyone notices what he's noticing. It's their job to see these things, after all. They're undercover agents, trained in seeing the subtle things, and they all see what he's seeing, and have seen it for years. Everyone who works in the LA branch of OSP, now and previously, see and know what Dom is beginning to understand. But things he wants to ask the others about are the questions You Just Do Not Ask.
Every single day, at least once during the NCIS: OSP conference call with Director Leon Vance, Sam Hanna looks over at his partner G. Callen when he has no reason to. When neither of them is talking, when he should be focused on Vance or whoever is speaking or the case, he's looking at his partner. Even when he has to look around someone else, everyone knows he's looking at Callen and not Nate or Kensi or whoever happens to be there. Sam's eyes are looking right through them.
When the team gathers to review what they know, Sam stands so he can watch Callen without anyone else noticing. Callen stands facing the screen on the side of the table closer to it, and Sam stands on the opposite and rarely takes his eyes off Callen's back. Everyone can see that his eyes are focused too close to be looking at the screen. Sam makes a call or pulls up information on the massive screen and Callen ends up at his side, though no one's sure if Callen's aware of it or if Sam sets it up that way without his help. Callen stands in the middle of the room, looking at the screen or talking to whoever is on it, Sam stands in one corner or across the room from the screens, so when the others are looking at either screen, he can watch Callen and appear to be paying attention.
Not that he ever isn't paying attention. Just because he stares at his partner obsessively doesn't mean he doesn't know exactly what's going on. Three years of watching Callen have taught him to focus on two or three things at once, and if you try to catch him staring or "daydreaming", as one probie accused him of doing, he'll rip you to pieces before you realize he's doing it. He's frightened more than one probie out of undercover operations and even out of NCIS with this technique.
When they interview a suspect, Sam sits at the table across from them, and Callen stands off to the side somewhere. Sam is too big, too intimidating, to be the threatening one. He's fully capable of frightening their suspect into silence with his size. This also puts him closer to the suspect, so if he pulls a weapon, Sam can get to it before Callen gets hurt.
When G. and Sam grill the new guy on the devil that is the details, they do so as a unit. They instinctively know what the other is going to say before they say it. Sam lets Callen lead, and keeps his eyes on the screen or the probie, points out the tiny details that they haven't caught because they don't have the experience Sam or Callen do. It's one of the two times Sam doesn't watch Callen.
There's no video camera inside Sam's car, because of stakeouts and the fact it's his private car, but everyone assumes Sam watches G, there too. The other members of OSP sometimes wonder how he doesn't crash. There's even a long standing bet between a few of them that if Sam ever crashes his precious car, it'll be because G. is in the passenger's seat.
The only problem with their theory is Sam doesn't watch Callen when he's driving. Or when they're on stakeouts. Or anytime they're in the car at all. He makes origami animals out of G.'s sucker wrappers, then keeps his eyes on the animals when Callen can't figure out what it is and says so, then doesn't believe him when he tells him what it is. He taps elaborate beats out on the armrest, though he doesn't do that much, because Callen accuses him of being twitchy. He recites all the parts of every type of firearm he's ever disassembled in his head, in order of importance to the function of the weapon or alphabetically or by size. He does anything but look at Callen, except when he finds excuse to threaten him. Sam's afraid to look at him. He's afraid of what being that close to Callen will do to him, or what he'll do to Callen, if he isn't careful.
Everyone knows Callen crashes on Sam's sofa sometimes. No one questions when Callen comes to work smelling like Sam's home, or, rarely anymore, wearing one of Sam's shirts, though they're far too large on him and Hetty throws a fit about him dressing like an orphan again. No one wonders what Sam's wife, who none of them have ever met, says about the younger man sleeping in her home, though they all wonder what she thinks about Sam's staring. Likewise, no one questions why, even when G. doesn't stay with him, Sam always seems to know what motel, or who's couch, or which room of the office, Callen has claimed as his own on any given day, when he'll decide he doesn't like it, and why he decides he doesn't, as well as why he didn't like the last four or six. They don't ask why he's so eager for G. to find a more permanent residence either.
When Sam and Callen clear a scene, Sam almost always goes in first. If they're going into a lead storm, he'd rather be hit than have to hold Callen while he bleeds out again. That way, at least one of them will survive mostly unscathed. They all know if Callen dies, a massive piece of Sam will die with him.
When shots are fired, the first words out of Sam's mouth are 'G.' or 'Callen.' When Callen was hit and almost died, Sam cradled him across his lap and begged him to not die. Though everyone in the office could hear, no one says anything under fear of death. When anyone mentions his case and the fact it's unsolved, murder howls out of Sam's eyes and his shoulders go tight, and whoever was speaking shuts up, unless it's Vance.
When they're in the field, Sam won't let Callen out of his sight. When he doesn't have a choice, he's never far from the building where G. is working. He used to work in the office with Eric, while Callen worked more with Mace, but since the most recent time Callen was almost killed, the time that left the scars across his chest and back, Sam has moved completely into the field. He reassigned himself to being Callen's full time partner. He managed to do this under Hetty and Vance's noses without them noticing until he was already more a field agent than a desk jockey or screen runner, and was ready to take his place as Callen's partner by the time he got back from his enforced vacation. After all, without Mike, they needed another field agent with the kind of experience Sam has, and he isn't afraid to point that out.
Everyone sees what Dom is seeing now, and everyone knows why Sam does what he does, except maybe Callen, who still appears to be oblivious.
Whether or not Sam realizes he's in love with Callen is up for debate.