[...]
PS: During the first search, the disk is heavy used (iotop) by writing from slapd.conf ... why it - should only read ...?
This does not make sense. slapd should not *write* to slapd.conf.You should probably learn how to use strace to find out what really happens on your system. You should also install the same LDAP database and the same config on another physical server to see whether it behaves equally there. If you can present proof that slapd is indeed writing to slapd.conf, you should probably file an ITS.
Good luck with your troubleshooting, -- Bjørn