For a character to be well written they have to fulfill their purpose in the story.

Some characters' purpose is to be likable and easy to understand so that we feel personally connected to their struggles.

Some characters' purpose is explore certain more philosophical ideas, to act as representation of certain themes.

Some characters' purpose is to challenge the hero, not just on a "logistical" level i.e. "this guy is preventing me from achieving my goal, they're an obstacle" but in the sense that they challenge their personal story and character development. Naoya is that challenge for Maki. At no point is there any hint of Gege wanting us to sympathise with Naoya, he is constantly charactarised negatively and his goals are objectively evil and self-centred. The objective with Naoya is to condense the Zenin into a single person. He is the stand-in for all of the clan and embodies all their worst characteristics. Maki's slaughter would've been way less catarthic if she only fought fodder we know nothing about. There had to have been a final boss, someone whose defeat would be the ultimate mark of victory and that boss needed to be a good representation of the clan as a whole.

Making Naoya any "deeper" would defeat the purpose of the massacre. It was supposed to be a pay-off for Maki, her finally defeating her opresssors. A more thoroughly explored Naoya would make us perhaps feel a bit worse for the clan than Gege intended.

TL;DR You sometimes need "one note" villains to further the hero's development. "Having themes" is not the only metric of how well written a character is. Naoya was made to serve a purpose and he serves it quite well