OS: Win10, 64bit
Okay, it's getting weird:
Launched KSP in 32bit mode and now I've the missed directories
└───PluginData
└───KerbalImprovedSaveSystem
config.xml
but there is no config.xml file.
I'll will do a KSP-fresh installation after my current game is "finished", do not put too much work into my issue. Maybe it's a problem with some other mods.