The directory module changed the URLs of categories

All my existing category terms are already URL-aliased based on pathauto:

categories/directory/shopping
categories/directory/school
categories/directory/party-event

and so on.

When I use directory, those terms become something like these:

directory/71
directory/252
directory/84

So is there a way to retain the original URL-aliases instead of changing them like that? I'm afraid Google is going to penalize on the search engine because of the duplication of directory/71 and categories/directory/shopping.

Plus, I notice when you un-collapse the vocabulary, it shows ALL the terms and subterms.

So if I have taxonomy structure like this:

-vocabulary1
--term1
---subterm1
---subterm2
---subterm3

When I uncollapse vocabulary1, it shows the term1 AND subterm1-3. Is there a way to show only term1 when you uncollapse vocabulary1, then show subterm1-3 only when you click the term1?