So, a closer look into the upgrade script revealed, that my situation (having ldap config without prefix used to be normal) had already been contemplated by alexAubin, thus modifying the setting ldap_config_prefix from ldap_config_prefix: s02 to ldap_config_prefix: '' was sufficient to take advantage of the upgrade logic and smoothly transition to 32.0.6!
# Before NCv32, Yunohost was not using any prefix for the LDAP config.
# This is now mandatory so we need to create a new config with a prefix.
if [ "$ldap_config_prefix" = "" ]
then
ldap_config_prefix=$(exec_occ ldap:create-empty-config --only-print-prefix)
ynh_app_setting_set --key=ldap_config_prefix --value="$ldap_config_prefix"
fi