Shaders are script files generated dynamically on the fly based on the needs of the materials/lighting/geometry etc.. they control how lighting sources, shadows and textures interact with the geometry and how geometry is mapped to the screen, for example, so the "preparing" step is pre-compiling the necessary ones, rather than trying to dynamically compile them when needed.
Earlier versions of the game were doing this dynamically, which is why there was a "hiccup" approaching a planet as that planet's shader got built and compiled. e.g. If your current system has no gas planet, there would be no need for the gas giant shader, but if you warped to one, the earlier version of the game built and compiled it as I approached it (at the visual point it would stop being a "small star" and start to look like a planet), this caused hiccups, so rather than do that, build all of them upfront, needed or not.
Modern shader programs get pretty big and compilation can take some time, particularly on AMD machines. You may not find them anywhere on disk, the script generation is really fast and there's no need to save that, only the binary result, which, given the constant upgrading of GFX drivers, windows patches etc.. etc.., is safer to recompile for the time being, as some versions of some drivers don't save it.