None of my players questioned how the crew got out. They assumed that the crew got out a while earlier, before the ship was as far underwater as it was now and there was more emergency power left. They explored the ship as best they could, gathered some resources, escaped out the roof, and are now hunting their kidnappers across the Islands subsectors. I didn't really follow the script at the camp, as I was setting up stuff for my actual campaign and the bugs were just local color to the NPC interactions.
I'd have to look it up again to be certain, but my recollection is that all air locks have manual controls. Emergency escape requirements and all that. But even if the crew had to use the manual controls, they'd still have to shut it behind them to open the outer door. So the PCs wouldn't be n a different situation. The fact that it has settled and is now underwater is easily explained as a change in the situation from when the crew left.
