So let me just ask you (I don't know if you're a man or a woman) anyway if you're a woman what would you think of your soon to be husband keeping something like that from you? If you were to be married to that person and then they told you and you involuntarily became a step parent boom like that, what would you react like?
Her whole thing wasn't about him having a son it's him lying to her about it. Think of it logically. There was no reason to keep this from her. Thea knew, Barry knew and Malcolm. All three of those people made it WAY more dangerous knowing than Felicity would ever have. It was a stupid plot most likely used to make Felicity look bad. I have my opinions about that.