This division led to the growth of different cultures, and even today this division is more than just "skin deep" to the Nikto. But this is a barrier that they have overcome. The species was able to unite together and overcome their differences shortly before the Hutts made first contact with them, and then helped the Nikto become a spacefaring species.
Religiously, their kind has had a cult oriented sacrificial religion base. And these different cults rise and fall in popularity as each new discovery the species makes influences their beliefs. The sacrifices they once made are now no longer a part of their religion, as they have been able to mature past that, as they did with coming to cope with the species' diversity.