after some experiments I solved the problems described above. It seems that conf/slapd.conf.in was simply missing the lines:
After this change and restart all users reappeared and LDAP returned to business as usual.
Note: Before this change I de-installed and re-installed admin extensions zimbra_posixaccounts and zimbra_samba, but I don't think that is necessary.
Nevertheless Zimbra's update mechanism should be changed not to erase such (advised) changes in slapd.conf.in
Sincerely - blue4koala