By definition of density independent, I would say it has an equal affect on large and small ecosystems.
I interpret density independent limiting factors to be factors that affects an ecosystem regardless of the population size. Examples could be: Weather patterns, natural disasters, and changing seasons. None of these are effected by how big or small an ecosystem is, they occur because they are fundamental to the principles that guide our world.
Density dependent limiting factors, just for a quick contrast, can be things like disease, predation, and competition. These are highly dependent on the size and density of a population, since disease spreads faster in small environments that are densely populated, predation is more devastating to a small population than a large one, etc.
