depends on the type of file you are attempting to add to your iPad.
Music/Movies/Apps/eBooks(epub,pdf) are kept within iTunes itself. photos are not stored within iTunes.
if you are really concerned about the file security I would recommend using an app such as Goodreader which allows you to add files to the app through either wifi or drag and drop the files into the app via iTunes. the files are not stored within iTunes, you just use iTunes to access the Goodreader app.