So, I'm stuck on Onderan as I can't finish the murder quest. I know where Nikko is supposed to be, but there's a completely different NPC in his place. I thought his skin was just being replaced like with Kiph, who's now a female twi'lek, for some reason. But unlike with female Kiph, I can't have a conversation with the NPC in Nikko's spot.

So what alterations / modifications have you installed?

Armor, reskins, romance, and weapon mods. The reskin mods that I downloaded were all for the PC and companions, though. I also have the restoration mod, which is at 1.8.5. I installed a cantina mod as well, but it says that the mod is for Nar Shaada. I also installed a mod for more rooms in the Onderan palace. I moved the override folder to see if it would bring Nikko back, but it never did.

That's because the data is stored in your saved games. With an issue like you stated, and all the mods you have, it's pretty clear where the problem lies. This is one of the pitfalls of using mods, especially multiple mods. I really don't see any way around this other than reverting to a prior save, preferably with mods removed.