There is that look between Kenway and Lolani at the end that suggests something. And then Kenway excuses himself after the beam out. From that point on different scenarios are suggested.
- Did Kenway already arrange a way for the ship to blow up and with Lolani's sanction knowing she would die also? (I think this is the most likely scenario)
- Did Kenway beam Lolani somewhere else and sent Ferrigno back to his ship? Problem with that is Ferrigno would have immediately began demanding Lolani's return.
- Even if Kenway got her hidden away somewhere he now has a problem of getting her off ship later.
- It's hard to imagine Lolani managed to blow up the ship herself given how she would have been watched and likely secured. Unless, perhaps, Kenway engineered a way for her to get loose.