The only way to stop that behaviour is modifying packages/mediacenter/kodi/tmpfiles.d/kodi-userdirs.conf in the build-system and then building a custom image with the modification. In our standardd image they will always be recreated on boot (by systemd not samba).
You can probably hack a delete via /storage/.config/autostart.sh but since this runs at the start of userspace boot you'll need to background the task for aa few seconds, e.g.