I hope my system has now no lasting damage by apt-get update/upgrade/dist-upgrade and "apt autoremove".
I hope so too but to be sure you can make a backup and restore on a fresh and clean installed Ubuntu 20.04 (or whatever you're currently using). Just make sure to restore to the same OS and Cloudron version and you should be fine. There are also guides what to do after a (planned) dist-upgrade so maybe check them out.
Funny, I just noticed this as well the other day but I figured it was just me because I'm running macOS beta so thought the new Safari overhaul killed something. haha. Glad to know it's a known issue and already fixed for the next release.