I don't see an obvious problem with the above.
It's possible your ldap.conf is being overridden, but the command-line options will take precedence, ldapsearch will ignore BINDDN in the main ldap.conf, so the only parameter that could be wrong is the URI.
(The order is ETCDIR/ldap.conf then ~/ldaprc or ~/.ldaprc and then ldaprc in the current directory, though there environment variables which can influence this too, see man ldapconf.)
Try an explicit URI:
ldapsearch -x -W -D 'cn=Manager,dc=example,dc=com' -b "" -s base -H ldap://localhost
or prevent defaults with:
LDAPNOINIT=1 ldapsearch -x -W -D 'cn=Manager,dc=example,dc=com' -b "" -s base
If that doesn't work, then some troubleshooting (you'll probably need the full path to the slapd binary for these):
make sure your slapd.conf is being used and is correct (as root)
slapd -T test -f slapd.conf -d 65535
You may have a left-over or default slapd.d configuration directory which takes preference over your slapd.conf (unless you specify your config explicitly with -f, slapd.conf is officially deprecated in OpenLDAP-2.4). If you don't get several pages of output then your binaries were built without debug support.
stop OpenLDAP, then manually start slapd in a separate terminal/console with debug enabled (as root, ^C to quit)
slapd -h ldap://localhost -d 481
then retry the search and see if you can spot the problem (there will be a lot of schema noise in the start of the output unfortunately). (Note: running slapd without the -u/-g options can change file ownerships which can cause problems, you should usually use those options, probably -u ldap -g ldap )
if debug is enabled, then try also
ldapsearch -v -d 63 -W -D 'cn=Manager,dc=example,dc=com' -b "" -s base