Why does this kid call his parents by their first names? I've always wondered about that lol.
I prefer this actually, like ain't it better than mom and dad? They don't have women in that world but it doesn't mean they don't have the concept of mother perse, them being basically animals and so on. So, I would find it kinda strange if koto is mom or if one is father and the other is dad or whatever variation you come up with.
Now, culturally speaking, I think the way Japanese people speak can be a bit formal for foreigners, even in couples. I think sometimes even old couples still call each other with -san, but I doesn't mean they don't trust the other person or they aren't close, it's a manner of speech or even that they are just used to it.
Now going back to the manga, there is also a possibility of koto and nagi never mentioning the word mom and dad to Yua, like when you say hello to the baby and telling them you are mom? Seeing as Yua basically came out of the egg as a toddler dragon that later on became a toddler human like being, he could just call them based on how they called each other while Yua was still an egg, nagi and kotone, Yua just can't say the full name at the beginning and it just stuck.
And i never want it to end