Currently the API works differently than the UI. in the UI a user can see files/folders that were shared with them from an external (to the org) account, however, when trying to query for the visible items via the API these do not show.
In addition - if you try to get the details of specific items shared by an external user you get an error when using the API, which is unfortunate since this causes 2 classes of behavior that are inconsistent between the UI and the API.