So apparently everything is fine. The NPCs did not glitch out or anything. They will appear for your normally in the story once you finished the final attack. It's still kind of confusing that they disappeared without a word. Especially since I reloaded older saves where they were still there and there they also disappeared. So I really suspect that this is a bug that is triggered by you doing something in game. Like maybe taking on another quest or finishing it, or leaving camp or something.
I also found the final fight to be rather easy.
My crew is level 8 I think, just as a reference.
