Serena Southerlyn's infamous "Is this because I'm a lesbian?" seems moronic, until you realize that the whole point of Law & Order is that you have absolutely no idea what goes on their personal lives. This actually becomes less true after her departure, but up until then it was a miracle if we knew anything about anything that wasn't strictly work.
Also, considering the fact that Jack McCoy had seduced/fallen in love with four out of five of his previous assistants, it does show his sweet but odd behaviour towards his current assistant isn't necessarily sexual - it's just how he is - because he treats Abbie Carmichael and Serena almost identically.
The last relationship Jack McCoy had with an assistant was with Claire Kincaid. Kincaid was killed in a car accident after going to pick up a drunk Detective Briscoe. He felt tremendous guilt over her death and kept the rest of his relationships with his assistants professional.
But fanon says Abbie's gay as well.
Only because lots of fans want to see her with Olivia Benson. Which would actually be the hottest thing ever, so no complaints.
This piece of fanon comes from the same school of thought which ships Alex Cabot with Serena Southerlyn, which would also be incredible.
And Jack didn't seem to have any more idea than Arthur did that Serena was a lesbian.
There was one episode that gave a hint that she was gay, and that Jack knew about it. In that episode (near the end of her run) Jack went to Albany and successfully had the court overturn a gay marriage law, all so he could have the marriage between the defendant and his spouse ruled invalid so the spouse would not be covered by spousal privilege and thus be forced to testify. Although Serena was normally very liberal in her opinions and questioned Jack on his tactics many times, in this particular case she was clearly outright pissed and simply stated she was obviously not going to go to Albany to assist him. Uncharacteristically, Jack didn't even try to argue with her, which would make sense if he knew she had a personal reason to be outraged at his plan.