The math has always indicated that Rick probably isn’t Judith’s father, since Lori wasn’t pregnant before the end of the world, and she found out that she was pregnant not too long after reuniting with Rick again.
All in all, the reveal that Shane is Judith’s biological dad doesn’t come as a huge surprise, but the confirmation is nonetheless welcomed.
Sure, Mr. and Mrs. Grimes got at least one romantic night in a tent together (with Carl sleeping a few feet away), but only after Lori and Shane had been hooking up on a seemingly regular basis.
It was possible that Judith was Rick’s; it just wasn’t particularly likely.