I'm sorry, I can find no evidence of this, but I can find evidence against it.
It mentions completely rodoing the graphics for dreamcast, the graphics would not have needed to be redone if it was on naomi. Also, the article mentions Soul Calibur coming out on system 12, perhaps your memory just colored the game to be a bit better looking, maybe the screen was bad, maybe system 12 soul calibur wasn't all that bad (from what I remembered, it looked like a software rendered version of soul calibur, graphics were exactly the same but soul calibur on dreamcast looked like it had been put through a psx emulator, and I don't think the arcade version of soul calibur had the curvy straight line problems that psx games often had) but it really seems you're the only one who says there was a naomi version of soul calibur.