You've obviously missed a lot of the nuanced gestures that Dean Norris has thrown in, then, because regardless of where Hank has ended up with Walt, there have been moments where he seemed intent on dragging Walt into the investigation to trip him up.
Yeah, he was joking in the flashback, but look at his face. Look at his face when the Madrigal employee is mentioned as being under their nose the whole time.
They're subtle visual clues, but we've been supposed to think Hank has seeds of doubt planted ages ago.
But you also hate Skyler, so...
Hindsight bias...