They both have "check-acl" entry in obj.conf so removing them is not a solution.
es-internal ACL is added as follows:
obj.conf:NameTrans fn="pfx2dir" from="/mc-icons" dir="D:/iplanet/ias/server/work/B1/WINNT4.0_DBG.OBJ/lib/icons" name="es-internal"
....
obj.conf:<Object name="es-internal">
obj.conf:PathCheck fn="check-acl" acl="es-internal"
This shows that "es-internal" named ACL is added for lib/icons directory and its subfolders if any.
"default" ACL gives read,execute, info permissions to all users but restricts write,list, delete permissions to only authorized users. That is the recommened configuration for WebServer.
You can add new ACLs below these two, lets say you want only user "alhpa" to access dir1 in Web Server's docroot add
acl uri=/dir1";
deny (all) user=anyone;
allow (all) user=alpha;