[quote=Vongola_Hasayo]
Naoto and his mother are part Japanese. I thought that was pretty clear by their names. Naoto and Miku aren't exactly traditional Italian names ^.^¿
[/quote]

For his part, In-character Prospero has been using honorifics with Naoto and Naoto only mainly as an attempt to tease him. Since his mom's been calling him 'Nao-Kun' and Prospero doing the same thing made Naoto get irritated and tell him not to do that, he switched it to 'nii' instead, partially to be more irksome. He's speaking Italian at all times unless indicated otherwise and he (probably) only has limited knowledge of honorifics at all through travel and cultural osmosis.

If it bothers you a lot I'll stop it, but it's something I felt was in-character.