The early-access game Shadows of Doubt also has extensive secret-knowledge mechanics which must be carefully managed, with the additional complication that it ideally wants to keep in sync the knowledge of the player and the player character.
I had an opportunity to play it for a few hours. It's not perfect - it didn't always keep up with my deductions, and on one instance it leaked unknown info via the UI - but on the whole it succeeded at a convincing mechanic.
It has some tempo management to work through I think, sometimes crimes are too obvious to solve and others are essentially dead ends unless you brute force your way to the info you need (which means talking to every NPC randomly or fingerprinting the whole city). And as you said, sometimes you have made a deduction, like who someone is thus linking their other details, but it's not relfected in the UI.
I had an opportunity to play it for a few hours. It's not perfect - it didn't always keep up with my deductions, and on one instance it leaked unknown info via the UI - but on the whole it succeeded at a convincing mechanic.