It was probably a one night fling. Even serious guys like Wesker have to fall back and have a little fun sometimes Jake's mom probably just "thought" he loved her. Plus, according to Jake's age it could be possible that Wesker was actually sane in those years. You have to remember, originally Wesker was much younger when he joined Umbrella.
Though, you have to also remember Wesker had a huge master plan. Jake's birth may have played into it somehow for all we know.
As for the appearance, it's not just the nose. it's the eyes and eyebrows. The eyes and eyebrows both default to the same "serious" appearance. The skull shape is similar as well.