@Emia Since City Living released, I have yet to encounter a sim with a Japanese name whose family name comes first.
All of the family names of the sims I (well, my sims) have encountered so far have their family name come last (such as Ikeda, Yamamoto, Sakamoto, Shimizu, and Watanabe) with typical Japanese given names coming first (Masato, Nobuya, Ayaka, Genji, Akira, Sakura, etc.).
But if you want your sims' names to be family name first, you can change their names in CAS. For newborn nooboos, you just type in the family name in the upper row.
If you're absent when a nooboo is born, however, the game will automatically assign the second name as the family name.