Subdirectory and subdomain can be 2 different things. A subdomain would be something like this: sub.domain.com . Whereas a subdirectory is something like this: subdirectory.com/directory/
Deep linking is linking to any page that is not main page. It helps the inner pages page rank. Not easy to do most directories do not allow it or charge for it.
No. A subdomain is a new domain. The only exception to this is when some hosts give you a subdomain that is also found in domain.com/subdomain/ In this case you have an internal duplicate content issue (nothing to panic about) that can be easily taken care of with a 301 redirect to the subdomain. Brandon