I guess it depends if you mean he knows it and can prove it (in court) or just "knows" it in his gut. Right now he can't prove it, and the confrontation in the garage was just him acting on a (strong) hunch.
I think Hank and Marie don't/can't see Skylar's full involvement in this and think she's just a victim of Walt's diabolical schemes. So when she balks at helping them and fleeing Walt with the kids, they're dumb-struck because they don't think she's as involved as she is.