If a customer has multiple phone numbers listed in the Emails and Phones subtable, is it possible to search for customers by the non-primary number? It seems like only the primary number is on the main directory record itself.
You are correct in that there is only one field for an email and one field for a phone number that is stored on the Directory table.
As far as searching for customers by non-primaries, this should be able to be accomplished by creating a dedicated application over a flattened table between Directory and Emails — alternatively, you could create a search app over a join or just the subtable itself too.