Both small-angle X-ray scattering and X-ray diffraction can be used to obtain structure factors, though I imagine the wave vectors accessible to each are different (?). What are the main differences between both, and why are structure factors obtained using the former technique often plotted on a log scale in y (and sometimes in x too?), whereas that's not the case for the diffraction-obtained functions?
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Small-angle X-ray is a device to investigate the structure near the surface (1-100 nano-meters). The x-ray is a high penetrating measurement for the structure of whole crystal structure. Therefore, looking into the surface structure, we make the x-ray a glancing incidence angle (0.1 - 5 degree).
For a glancing angle x-ray, the diffraction intensity is, of course, much smaller that the larger incidence angle. In order to observe the diffraction intensities over a larger scale of magnitude, we use log scale. For example, the ratio of two diffraction intensities $1$ and $ 10^{-6}$, the weaker diffraction will be completely depressed in a linear-scale plot. The log-scale will be employed to observe both diffraction lines.
