Yes, it depends on what "Axis Victory" means. Having a few neutrals around is helpful if you still have to deal with your former enemies as independent entities. Since some "Axis Wins" scenarios allow for the survival of an independent Britain and most presume the USA survives as an independent power - often in a "cold war" with Germany, I could see certain neutrals (particularly Spain and Sweden) remain independent (although "finlandized") as valuable locations for unofficial contacts between Germany and its enemies. To my mind, it is less likely landlocked states such as Switzerland would remain truly neutral.
By the way, didn't Portugal join the allies?
Another consideration is the difference between wartime allies of Germany and nations which were occupied and lost their independence. Depending on the scenario and how Germany actually sought to structure its European Reich, allies or friendly neutrals such as Italy, Finland, Vichy France, Hungary, Romania, Slovakia, and Croatia might serve the function of neutrals in the diplomacy of the post-war world.
But I agree with CQ. No matter how things develop, all remaining independent nations in Europe would be drawn into the German orbit...certainly none would be permitted to be openly hostile to German interests.