In my router with OpenWrt I have the file /etc/ntp.conf. But ntpd package isn't installed, so why is this file present? Could it have been left there if ntpd was once installed and later uninstalled? Or is it just there by default? Does it have any effect the configuration on busybox's ntpd or is everything in /etc/config/system?
Yes, if you installed it before, the configs are saved.
No, sysntpd is configured in /etc/config/system; and both cannot run at the same time.