Yes and no, with a fresh install it will see all your files just fine, but until you install programs like itunes so that you get the codecs. Your computer will not know what the files are.
As far as your programs, Depending on how the program installed itself. Most will still be able to run off the other hard drives on thier own. Some programs install files to the OS drive regardless of install location, and with a fresh install these files will be missing and the program may not run.