There's almost certainly a name for the concept I'm gonna talk about, but I don't know it and I'm not gonna make up a name cause I'm not crazy.
But for all fiction, there are questions that just don't get answered and parts that just don't get talked about. They're not important enough to the story, or they contradict the tone, or they are just in some way uncomfortable. This is true though all of history, there's always some things just not brought up. Even in modern, exhaustive world building stories, not everything gets touched on. For an example, there isn't anything even in the Silmarillion about poopin'. We all know the characters do, but yo that's not important.
For Aika, I think a lot of the background evilness of the delmos falls into a similar category. For the same reason as to why a lot of the violence is consequence-free, it's just not really fun anymore if you dwell on that. It becomes far more serious if they killed 3000 people; but things still have the same light-hearted tone and they still humanize and moeify the delmos after the ship event, which just makes things uncomfortable if the show was also telling you "hey they just killed a 9/11 number of people you know." So it's not important. It establishes they're powerful and are able to do things, but the viewer isn't told the consequences and that's fine, because not everything has to be stated and it's more fun to be able to move past it and imagine whatever you want about what happened.
But to answer your question HurfBlurf, about what I think happened: I think the ship was automated. Maybe it's an old ship pressed into service that they refitted into being automated, and that's why it's big and got a bridge. Maybe they built it that way so it can be manned sometimes too. Why do I think this? Because it doesn't change the tone of the story too much. The supporting evidence I've got is that no one talks about all the lives lost on that ship, so it's perfectly possible to imagine no one was on it or that everyone was somehow totally fine.
But for your project, it's ultimately up to you. If you want a different tone, then go ahead, they killed 3000 people. But if you're struggling to keep with the tone of the anime and running into issues because you start thinking about the background and events and they're not adding up, well... it's totally okay to just ignore things or handwave things or invent things so that people are totally okay. Literally every story ever told doesn't say everything that's going on.