The key difference between Earth-1 and Earth-38 isn't just the presence of Kryptonians, it's the presence of aliens in general. Earth-38 has a sizeable population of alien immigrants from numerous worlds, yet Earth-1 has no known alien visitations besides the Dominators in the 20th-21st centuries and the Thanagarians in the 22nd. The fact that the Earth-1 US government didn't already have a DEO-type bureau, just the nasty Man in Black guy, suggests that they didn't have frequent enough alien visitations to justify one.
So the question goes well beyond Krypton. Why does Earth-38 get so much more immigration than any other world we know of? Given how many of the aliens on Earth-38 are refugees from war-torn or devastated worlds, I suspect there's some evil force out there that's been ravaging the universe. Maybe in Earth-1's universe, that destructive force isn't there, or is kept in check by the Green Lanterns (who are implied to exist through a reference to a disappeared Ferris Air test pilot), so the aliens are content to stay at home, or they go to other haven worlds that were destroyed in universe 38. And so maybe there's some alien race in universe 1 that was able to stop Krypton's destruction.