Alys wants to say she noticed right away, but of course that can't be true. In those first few terrible weeks she was grieving her husband and raising a newborn infant, not to mention doing what she could to help Cordelia and Aral run the Empire.
But Simon was there, always, working with Aral and doing whatever needed to be done for the Emperor. The only quiet moments Alys had were filled with tears or snatched sleep between the crying demands of her son or the apologetic ones phrased as requests from Aral.
Soon enough she did notice, how Simon always quietly apologised, how he always offered a favor with every asked one, how sometimes he would even take Ivan from her arms, rocking him to sleep or playing with him so she could focus on whatever missive he'd brought her.
Well before the end of her Mourning Year, she would have asked. Oh, she would have asked him the first time she finally noticed, blunt and to the point and not at all what a woman of her status and stature could have expected. A year after the whole horrible mess and Barrayaran High Society had rightly itself completely, and Lady Alys could have expected any number of well-prepared and well-paid offers of marriage.
She let it be known she was not at all interested, only had to refuse a scattered dozen -- most of which were obviously political, keen eyes for the throne through her. Only two were hiding attempts to replace Gregor with Ivan and those Aral and Simon quickly dealt with.
She was interested, though, in the one man who showed her kindness and courtesy and never once said a word about what she knew was lurking in his eyes.
Neither of them could. Aral needed Simon, which meant the Empire and the Emperor needed Simon. Alys could not need him as well, so she carefully detached her son from Simon's arms before he could grow to love him as a father, gently stepped back from that entire side of the politics and immersed herself in her own side. As Gregor's official hostess, there was plenty to do which would not let her dwell on things that could not be had.
She still worked with Simon, still saw him all the time, still carefully did not exchange a word or two that could be misconstrued.
The look in his eyes never vanished, but he never pressed. Alys never gave him encouragement to, until the day, decades later, when he knocked quietly on her door.