Hank Has To Know That Skyler Knows What Walt Was Doing
Remember Hank has known Skyler for 15+ years. So in addition to his nerdy brother in law being a ruthless drug lord, which is already

You ever heard of Dennis Rader? He was a serial killer in Kansas. He was married for 34 years and his wife never had a clue:
http://www.thedailybeast.com/newsweek/2005/07/10/married-to-a-monster.html
So nah, I wouldn't assume he thinks she knows anything. He probably thinks she got roped in by Walt's gambling story, just like they did.
Also, Walt tells him "what's the point?". He'll be dead soon, so why push this now? It's too late. Hank says "have Skyler bring the kids over, then we'll talk". Meaning, "ok, I see your point, but I don't want your wife/kids around you".
That's how I interpreted it anyway.
Fred.