I couldn't get that to work. I mean the syntax is good, but I got the same result. Its true that these are 0-length strings. So to make them NULL I changed the select query to:

case when ltrim(rtrim(mycol)) = '' then NULL else ltrim(rtrim(mycol)) end as mycol.

In the preview I saw the NULL value, but it still got quoted. Seems like the Text Qualifier in the flat file connection manager is overriding everything.