Game information is truth. Of course, how you roleplay that truth is entirely up to you. You can always deny it, Clinton-style. Then it means that there are persistant rumours that X is really a bastard of the Y family.
I don't think that using the family relation between characters is per se an SMA violation. This is a bit of a tricky area because while the family link is game-truth, the fact that these characters are played by the same player is not, that's OOC info, so even with the family link there, you are supposed to treat the characters as maybe related, but still different persons.