Rafe knew quite a bit about Sami and her involvement with EJ, which they talked about in WPP, and I think he already knows about the "elephant in the room" from back then.
The thing about having those talks happen offscreen is that it can be interpreted either way. We don't really know whether Rafe knows about Johnny's conception or not. We can choose to assume that he does know or assume that he doesn't know.
I understand the temptation for TPTB to leave such things open to the imagination because it gives them more flexibility down the road. However, the trade off is that it diminishes from the current story they are trying to build. I find it very difficult to invest in characters and/or stories that I constantly have to guess about. I could buy in to a "connection" between Sami & Rafe much more easily if these type of "bonding" scenes had played out on camera.