if I am the owner of a project and I am using this to store my documents and I want to restrict users which have access to this project from view all the documents but only specific document(s). Can it be do?

If you are member of owner company you can mark document as private. That way only members of owner company team will see it. Every other document can be seen and downloaded by the clients.

There is currently no such thing as "personal" object (visible only to the user who created it and marked it as personal).