I once said that I would never put Togusa and Motoko together in my universe. But then this plot bunny grabbed me, and WOULD NOT LET GO.
They never talked about it. It was just too embarrassing. Much easier to fumble and say the wrong thing at the wrong time than to actually talk about it.
For Motoko the problem wasn't very simple. Yes, Togusa was attractive. Yes, he was one of very few people, much less men, that could keep up with her on the mental plane. But he was married. He had children. Off limits, don't touch this.
She couldn't make herself stay away, though. She just leaned against the rail, watching him pull the targets in the range. Maybe he noticed her, maybe he didn't; he never glanced at her or gave any visible sign that he saw.
The longer she knew him, the surer she became that he never quite gave his all, and she was certain she had never seen any heavy slip of control in his emotions. He would certainly let his shock through, or disgust. But never hot rage, like Batou; or Saito's cold fury, that would leak from him and paralyzed everyone with terror. The closest she had ever seen him come had been his indignation over her ghost-infiltration key.
Togusa's problem was plainer, on the surface at least. He too realized that he was married, and completely infatuated with Meijiro besides. It didn't make sense that he kept on thinking about his commander.
She would follow him to the gun range and watch him. But he couldn't understand why. Aim, fire, reload, and repeat. What could possibly be so fascinating about that? And he would do it for hours at a time. Surely she had other methods of entertaining herself.
Besides, she made him nervous. Because Togusa lost it sometimes, in the range. Felt that inexplicable rage fill his mind and destroyed something expensive. He didn't want her to see him like that.
There were things they never talked about, boundaries they didn't cross. There were plenty of screw ups on both sides, and they could never be honestly and truly comfortable with each other since they had hurt each other so many times with foolish carelessness.
But Togusa once saved Motoko with some well placed bullets. And Motoko once kept him from getting thrown out a thirty-story window.
They had their problems, but then, so does every couple.