The Trivia of it on Elfen Lied Wiki mention it had some resemblance to the Super X obviously they can't make it 100% too close looking to the Super X without Toho suing them into the ground given how protective their I.Ps so of course they have a different shape to get around legal barriers but enough to look like the Super X for some to get the reference since it has the lights of the front and has similar shape in someshots as I have the Manga so let me get more shots real quick that look more closer to it a bit so let me get them real quick.
I don't know why you're putting such weight in a subjective observation. It doesn't even claim that it was a reference, just that it's "somewhat" similar, perhaps by coincidence. It sounds like you've just decided it's true and are working backwards to come up with reasons to justify it.
The only things I see them having in common are extremely nonspecific, like being vaguely spheroid, flying, and having headlights. There are far more things that are different about them. The Vector ship seems to be rounded all the way around whereas the Super X tapers on the top and in the back; its surface looks like a beetle's shell instead of smooth metal plating; it has at least five prominent lights on the front in contrast to the Super X's one; it appears to be biomechanical, as guts spill out of it when it's destroyed, which has nothing to do with Super X; and it appears to possess, or maybe project holograms of, giant humanoid arms, which also has nothing to do with Super X.
Unless you can prove that the mangaka had Super X in mind, I do not see any case for it.
You haven't sufficiently justified why we should. If some other wiki said that a bowl of spaghetti looks like Godzilla I wouldn't go adding that just to stop somebody else from doing it; that's silly. And I can tell you that I have never heard of this ship in my life. On the off chance that anyone else finds out about it and tries to add it, it's only one button to revert.
I decided shown it to people I know who are Godzilla fans to give secondary opinions to see if it was intentionally or not and they lean more towards yes the seemly thinking reference is intentional but the different shape and extra lights is done so Toho wouldn't sue the Manga given how protective with their I.Ps here so the slightly different shape and extra lights are likely just legal loopholes. So I just modified it to say it has a similar appearance with a different shape here.
Also arms aren't holograms they're Vectors the species Diclonius from Elfen Lied use that are invisible telekinetic arms as weapons and the craft can artificially use them here that was made from Diclonius remains hence the organic part.
Even if it was coincidental there should be at least some sort of mention here than just erasing all acknowledgement here.