[NiLuJe]

@arooni:

1/ A KOReader upgrade shouldn't affect your history (... unless you're doing a clean install manually or via the KUAL extension, of course ;p).
Otherwise, mostly everything sits in the settings folder, settings.reader.lua, the persistent defaults lua file, and the sidecar folders alongside your books (so, outside of KOReader's folder).

2/ No idea, a quick glance appears to point to reader settings (i.e., settings.reader.lua), like everything that doesn't live in defaults. Some plugins do use a dedicated file in settings/, too.

3/ That's not usually needed, no. You might need an extra restart for every hook to sink back in place, but that's it.