Look it's like this, here's a bio I had a lot of trouble finding, these dots are essentially single pixels, a couple of kms higher and they just vanish, there comes a point where the resolution level is so low you simply cannot see them from orbit, you have to cruise really low just to see them even on the dark side of the body.
They were nice once you got down though, very easy to find in the dark, but if you are to high above the planet the blue marks simply won't appear at all.
So it's not that they are small and hard to see from high up, it's that they are simply so small that a single pixel is to large at that distance and they don't show at all. I am well used to this sort of hunting, it becomes second nature once you get the idea, if you are doing it from orbit you need to be just above glide height, it's a difficult trick to master because without constant attention you can easily drop into glide, very annoying.
