Today I tried something which convinced me that this is a e-smith bug:
I simply changed the standard certificate from LE to the initial certificate (+reboot) and then returned to the LE as the standard certificate (no reboot). NS LE started to work and SoGo, Mattermost, Nextcloud and all the other services got the correct (most recent) certificates.
Please let me know if / how I may investigate / report on this issue.