If you read the manga and I gather that you have, it is made clear that Motoko is bisexual. I mean, she has a live-in dude but there also is a threesome scene wherein Motoko gets it on with two female cyborgs (I had loved Batou's reaction to being an unintended party to that!). In SAC, we don't see her with a man, but it is implied that she as "girlfriends with benefits" across the city.
As for Section 9, well... I don't know about the team (get to that later), but I always thought that there was an unspoken love in between the Major and Batou. That was when I memorized the movie; my thoughts only were strengthened by 'Innocence' - that Batou felt protective of the Major because of his feelings, and the Major knew it, but did not do anything about it (the closest she gets in the films to reciprocity). In short, there was an 'understanding' in between them that never needed words, or any sort of usual expression of affection to exist. It's THERE and that's enough for them (*sigh*).
In the manga, it is implied that Batou may fancy her, but he has other ventures and their personalities differ too much to be reconciled in an actual relationship. At least, that's what I recall, I'm not so sure.
In SAC, I think those who posted before me said it. Batou's into the Major, the Major knows it, but neither take it any further. The final episode of the 1st GIG (Batou's reactions to the team's comments) is clear evidence that he fancies her. As for the Major, well... she is more engaging than the cold shell she is in the films, closer to the manga version, and likes to tease Batou. The indication that Batou approaches to the subject, despite his feelings, rather casually is in 1st GIG Episode 15 - his choice of words for the Major's secret emergency meeting being "This isn't the proper atmosphere for a confession of love, either." given context, this becomes quite something else.
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