Well, it's not your overlay's fault. The same happens with overlay unique: It works, but does not show up in ldapsearch. Nor in the config directory written with slapd -f ... -F ...

$cat slapd.conf include servers/slapd/schema/core.schema database config rootdn cn=config rootpw secret overlay unique unique_uri ldap:///?olcAccess?sub access to * by * read

$ ldapmodify -xHldap://:3890 -D cn=config -w secret dn: olcDatabase={-1}frontend,cn=config changetype: modify add: olcAccess olcAccess: to * by * read -

modifying entry "olcDatabase={-1}frontend,cn=config" ldap_modify: Constraint violation (19) additional info: some attributes not unique

On the other hand, this is strange:

cn=config

• cn= schema
  • cn={0}core
• olcDatabase={-1}frontend
• olcDatabase={0}config
• olcDatabase={-1}ndb_pl
  • olcoverlay={0}ndbover

Two different databases should not have the same number. ndb_pl should get {1}. Possibly your backend or overlay messes up something in that regard.