Rukia's pretty observant when it comes to Ichigo. I think she would notice it. XD

It's my assumption from what I've seen of canon that while he has a strong similarity to Kaien, physically and personality-wise, she feels more strongly for Ichigo than she ever did her former taichou. I think while they remind her of one another, she keeps them very separate in her head. Not only that, but she'd always thought of Kaien as being untouchable, because of his wife, whom she looked up to - and Ichigo is not. :)