Will the source of natural fuel that Starfarers collect fuel from (i.e gas giants) be relatively close to safe space? Also, will the amount of Starfarers collecting at these sources affect the output/production? Will these resources ever run out for a particular location?

Cloud Imperium

There will be gas giants throughout the galaxy; roughly 75% of the star systems we have built to date include at least one. The number of Starfarers shouldn't really deplete them: gas giants are very, very big!