Maria didn't know how Cap knew, or even all of what, but she also knew the value in letting him take his time to run people to the ground, do his work outside of official SHIELD communications. Especially given this bit of business coming to light; the less he communicated with them, the safer everyone was and the more likely Hydra would be caught unprepared for the very cranky American symbol. It didn't make her comfortable, but it was a part of how the spy game worked.
"Could be from the Winter Soldier," Maria agree. "You go back as far as those two do, you start seeing patterns in their activity; Winter Soldier gets activated, kills someone high profile, ask 'Where's Hydra'?" She shrugged a little, drumming her fingers on her coffee cup. "Then you know, and they don't know you know, and that gives you a considerable edge. You just have to keep from letting them know that you know, so you move careful, and you keep out of sight." It didn't really matter how he knew, just that what he was doing was obvious, when you had enough of the pieces and knew enough of the players and the rules of the game, even if you didn't have any piece directly on the board.
That could change, though, particularly as they'd dragged over her gameboard and were placing their pieces on it while she hadn't been playing on that board. It was one thing to be aware that double-agents and moles were always a thing, even in her organization; it was another entirely to realize they'd scored some points while she'd been busy with a different board. Curse of being Director of SHIELD, she figured.
"The people he's fighting aren't exactly playing with rubber bullets and toy knives," she said dryly. "They're also not people who the courts can handle, even if they could be charged and agree to sit in jail until their trial." But then, the place where she'd always deviated hardest from the Bats of Gotham was what constituted appropriate force towards threats.
Of course he was already doing things, and Maria nodded approval, and not just because there were little bundt cake pans going into the oven and Alfred tidying up the counter. "If they took someone bleeding with them, it's for a reason, they took him for intel purposes. Impossible to say which one, but if we're lucky they grabbed someone who knows something about who they've got in SHIELD. I can run a quiet check on who accessed what when I get back, see if a flag pops up."
She considered his plan, then grinned. "I like how you think. In theory care would have to be taken as to who knew about about finding Nygma, but it's a workable plan. You should come play for my team."