Since the Google Apps Profiles API has been officially deprecated. It has been replaced by the Directory API. The fields (Organizations, Phones numbers, ...) of a ContactEntry (Apps Profiles API) exists in the User (Directory API).
But I cannot find the UserDefinedFields and ExtendedProperties fields in the User of Directory API ?
How can I have access to these kinds of data ?
The Directory API exposes custom Schemas. Your app can create a Schema object and define the fields supported by that schema. Then you can include json to set fields in that schema. However, the fields are associated with that schema. The intent appears to be to expose those fields to custom apps, not as part of the data shown for a user in the Contacts Directory. If you had code which set UserDefinedFields on a user's profile object and were visible in the Contacts directory those fields are not visible to the Directory API. It also appears that you can't use Directory API Schemas to add user defined fields to a User that will show up on their profile view in Contacts Directory.