I've been thinking about this as well and have some thoughts.
First, I think it's possible that one or two at least will discover they are in the next update, it makes sense for it to be part of the climax of part one.
Second, I think it's likely that the Sovreignty girls (I would include Jade in this) had been receiving regular birth control (injections most probably) as part of their standard medical package. A military wouldn't want its soldiers and officers (or their "servants") getting pregnant all willy-nilly. So, in that case the early sex with Céline and Jade wouldn't have resulted in pregnancy. It's likely that the three-month skip worked all that out of their systems so the sex since then could result in making babies, but it hasn't really been long enough to be noticed. Also, outside of that three-month time skip, only a few weeks have gone by. So, Thyia (who was also frozen for those three months iirc) may not be aware she is knocked up yet if she hasn't missed her cycle. And you don't even get sex scenes with most of the other girls till very recently in game time. Now, even in the real world it's possible to detect a pregnancy within a week of conception so they could probably tell the day of with future tech, but they would need to be looking for it.
I think it's highly probable that Aven will announce a pregnancy in the next update (if you've chosen to do it) just before Nadya makes the truth of everyone's relations plain. This could cause some tension since she seems to still be uneasy sometimes about being cousins, how much more being siblings? It's also possible that Céline might come out as pregnant as well, especially if you told her to be upfront about your relationship, and this could all lead to the confrontation of the MC's actions of hooking up with everyone. Could even be why he's floating in space at the start of the game. Maybe they make him take a walk outside the ship while all the girls figure out how they feel about his action. It would be a funnier way of getting him into the predicament we see him in at the start of the game. Though he might end up alone in a suit for any number of reasons, I think any antagonistic force wouldn't space him in a suit, they'd just space him. Makes me think he isn't alone in a space suit because of anyone with nefarious intent.
