To Get the Search Items from the sub folders of the list using SPQuery you can do following
SPQuery.ViewAttributes = "Scope=\"Recursive\"";
However this is undocumented/non public information so MS can change it any time in the further releases and you code will start breaking.
Instead, one can use SPSiteDateQuery class to search across multiple Lists. you can go to my blog for further detail and example.
http://www.sharepointblogs.com/akhileshtiwari/archive/2007/10/11/query-multiple-lists-using-spsitedataquery-class.aspx