Where and how does drupal store the node body in drupal 7?
If you emptied out the field_data_body (and revision) table and you are still getting data that can only mean three things: 


you emptied the wrong table (wrong database or the right database with the wrong prefix) 
it's still cached (there's a clear cache button on the admin/config/development/performance page).
You are not using SQL to store your fields. Do you have mongodb_field_storage enabled? Something even more exotic?


As for how it gets stored, node_save calls field_attach_insert (and node_load calls field_attach_load) which, in turn, calls the field storage module which I presume is field_sql_storage and so field_sql_storage_field_storage_write writes your database records and field_sql_storage_field_storage_load loads them.

Also note that array_shift(array_keys()) is wrong (E_STRICT error: Only variables should be passed by reference because array_shift takes a reference and array_keys is not returning by reference. Finally, you should feed your EntityFieldQuery code to the coder module to fix the coding standards: at least the code inside the if is indented wrong and the string concat operator (the dot) needs spaces on both sides. It hurts my eyes :)