"Frequency" does affect the frequency of bases. Also, those bases are smaller if more frequent, and larger if less frequent.
"Size" does not affect the size of the bases, seemingly at all.
"Richness" does not affect the size of the bases, seemingly at all. - EDIT: This part is by design. "Richness" affects how dangerous the biters are, not the density of spawners within a base.
Below are 2 images, one from "Very Big" and one from "Very Small" bases. I have not labeled them. They are exactly alike. Changing the richness settings would generate the same map.
![Image](http://pulpaudio.com/factorio/verybig.jpg)
![Image](http://pulpaudio.com/factorio/verysmall.jpg)