I found something interesting in the Youtube comment of this video:
Huh, I suddenly realised that Xemnas' power over nothingness actually makes sense. He has power over "nothing" a.k.a Dark Matter. The state of "nothingness" doesn't truly exist, as energy is eternal and it merely converts into different forms instead of ceasing to exist. So his power over "nothing" refers to how he can manipulate energy that is in the form of "nothing", which is Dark Matter and possibly something else as well.