I think Broccoli
has made some excellent points.
I think Richard knew of Jason's, umm, "super" parentage by the end of the film or at the very least had a very strong clue. Think about it. Richard was Jason's father for five years , and you'd have think that in that time Lois would have told him... not doing so would have been maternally dishonest and seemingly out-of-character for this particular, more matured version of Lois. And judging by the events of the film, I think Lois knew that Jason was Superman's son far before he threw that piano, understated reaction or not. How could she have not?
I also think it is perfectly logical for Richard to assume the father role, much as he does in the film, in Superman's absence. I grew up in an almost identical situation to Jason (sans superpowers... so far as I know, at least), where my real biological father was absent for most of my formative years and the man my mother eventually fell in love with, who would become my stepfather, I came to know as my "Dad". To the point where to this day I appreciate and love my stepfather even more than my actual one. As a kid, I even called him "Papa".
My point is, it is perfectly logical to assume Richard knew and thinking about it does reform my thoughts on the film and makes me view it in an entirely new and more appreciative light (...and I loved the film to begin with...!). It just shows how deftly Singer handled the whole issue, and him being an orphan with adoptive parents himself, you know, it makes a lot of sense.