I hate to wade into the pool of systemd hate, but is this systemd's fault? I noticed anacron doesn't exist on this system. Is it supposed to anymore? Or is that one of the things that have been deprecated? If so, how are the /etc/cron.daily jobs getting run these days?
You'll have to check the timeframe of when these changes happened with respect to Debian 8, but a Debian 9 system does not use cron to run anacron and various other things like phpsessionclean, nor use anacron itself to run various further things. You'll find [ ! -d /run/systemd/system ] in various places in Debian Linux nowadays that turns stuff off when systemd is running, as well as reliance on the fact that systemd ignores non-native stuff if it has native stuff of the same name (such as anacron.timer).