Regrettably, a massive interstellar Hatology conference was in session on Earth the very day the AI struck, and the art of hat-simulation was lost to humanity.
That said, there are a few things that should hopefully help them already not look the same:
1) There are 4 different "forms" of the shadow ship, each from a different race (and different sizes of each of those 4, though presumably everyone will use the largest available to them most of the time), and those look very different. The different forms have different advantages, though that's still in progress (only 3 of the forms are implemented at all at this point)
2) The far-zoom icons for all of them use your player color heavily.
Personally I'd be happy to add some visual customization, but I don't think Chris can spend a lot more time on the art for the expansion. In theory some kind of paid-DLC could work for that, but it seems weird to distribute the art to everyone (which we would have to for it to display correctly on everyone's screen in a multiplayer game) but only enable the interface option of choosing them for people who've got the DLC. They could instead just copy the new asset over the old one if they really wanted to see it, rather than paying for it.