Default out of the box installation of Windchill will store all the files in the DB as BLOB, since dbs are not optimal for storing large files, PTC recommends to switch to file vaults by setting a property(s) in wt.properties. When you use file vaults, the database stores just the metadata(think of it like a lookup table) and actual files goes in to file vault. The name of the files in the file vault are based on a hexadecimal sequence and the lookup for this is in the database.
The local LDAP stores configuration information as well principal information. The configuration information includes naming services, task delegates, the principal information includes administrative users, Organization, users to group and group to group information. So you can't get rid of LDAP
