He did, at least 2-3 separate occasions.
You aren’t shown those by the media, but the threads here posted them, at the time.
I’ve been hearing about this so I looked it up. He may of shaken her hand (or not) but they seem to be referring to a point at which Merkel specifically asked him to shake hands and he didn’t reply. Accounts vary - it was loud and he didn’t hear the request or he intentionally ignored her. I’m willing to guess he ignored her because he is establishing that she, as her country’s representative, is socially in the dog house for decades of shafting the US.
http://www.usatoday.com/story/news/politics/onpolitics/2017/03/17/angela-merkel-donald-trump-handshake/99310398/