3.12 implies that they are. So…are they?
Episode 3.12 is actually the 42nd book in the Frontier Saga. If you read the very first book (1.1), you will get all the info about your question!!! It's a definite YES.
I know, I’ve been a fan from the beginning. But ever since that first tryst, they had just been friends. I mean when her original body was killed, there seemed to be something there based on his reaction. But I was take a little by surprise in 3.12 when she all of a sudden was sleeping in his room.
In part 1, she kissed him before getting in the jump sub before her Tau Ceti insertion. Played it off as a joke. In part 2, I think in rescue, they confessed their love for each other on the Jung hone world. Again, in part 2, in Balance, they are bunking together on the original Seiiki. Doesn't explicitly say they are intimate, but after Rescue, it would not shock me. I've been re-listening to the series from book 1 and that is as far as I have gotten. I think there may be more later. They've always been flirty. The founders day night is mentioned several times in part 1. It is also mentioned when Nathan is getting his memories back. He tells Jessica that he'll review that one again later.
I think it stops when Nathan takes command again until 3.12. I also think at one point Nathan mentioned retiring to a cabin with Jessica.