So if the Commander is human and a kanmusu is mostly mechanical or magical, what is the byproduct of such a union? A cyborg or homonculi?
I don't think it's like that. I think that what separates the shipgirls from the abyssals is that the shipgirls have their mechanical parts and their biological parts separated. This allows them to have personalities and a greater sense of identity. While their bodies are created through spiritual magic, they are not magical. The mechanical parts which they carry into battle represent the hard shells of the ships they were in their previous lives, while their bodies are shaped by the souls of their captains, crews and the cumulated karma from actions taken in their previous lives. Their souls are created from the joy, courage and love of ship, country, comrades and life that the crewmembers experienced during their service.
On the flip side of the coin the abyssals' souls are shaped by the despair, fear and anger that the crew would have also felt during their service, especially when taking that last water-filled breath when going under. As a result they are an abhorent mess of mechanical and biological fused together. They lack a clear identity and have no peace of mind. In their constant mental anguish they seek only destruction and revenge for past transgressions that even they themselves can't remember.
So in short, I believe that their bodies are 100% human (though shaped from spiritual energy) and thus their children would be too.
Always got the impression that the Kanmusu were superhuman in capabilities. I mean, if they are just regular humans at the end of the day, what makes them so special? Sure, they would have all that emotional baggage and experience to give them an edge, but I think others would be more qualified, like maybe spec ops.
My head canon likes to rule out any mystical stuff at all and rely on the more alien and otherworldly aspect of it. Kanmusu are able to fight abyssals because they are humans infused with reversed engineered tech from abyssals. They take on the name and mannerisms of old ships as a form of respect and good PR. The human abyssals take their form as a way to demoralize their enemies and mock them.
Certainly not the cleanest way to play with the canon, but as someone who loves X-com, it makes it bearable.
I prefer the spiritual idea. It's loosely based in Japanese culture and shinto religion (thus it makes sense from a Japanese developer too). When I said that they aren't magical I didn't mean what I think it seems that I meant. What I meant is only that their bodies are biologically identical to humans. However, they do have some spiritual connection to their mechanical part, which allows them -and no one else- to use its power. However, when they aren't using their mechanical part they don't have any kind of powers and are just like regular humans.
Not arguing against your headcanon (What's there to argue? Headcanons are personal), just clarifying my own (and linking to interesting reading material).
That is most likely what the real canon is anyway, so I've always had that idea of a spiritual connection.
That being said, Kantai Collection is a franchise where half of the things I like and the other half I don't like. For example, the game itself is alright for a F2P, but the anime is an absolute dumpster fire. Having ships come back from the dead is cool and all, but having them actually act like ships in battle is pretty dumb(just look at that Akagi meme). The doujin and fanart community is poppin', but the developers can't seem to get what the fans want (Enterprise). If it weren't for the fact everything were so ambiguous, like Touhou, I can't see it having half of its current popularity.
The Akagi meme? You mean the meme that she eats a lot? She doesn't do that in battle though. What do they do in battle that doesn't make sense? Perform ship tactics? Why wouldn't ship tactics make sense? It's probably all they know anyway.
Personally, I don't watch the anime for the story. I just watch it to see the characters animated and interacting with each other. The game is just too static in that regard. The characters all have interesting quirks (though the anime overplays them as much as the fanart does) and it's fun to see them in a social context.