If the unpacker actually does unpack everything, deleting the .paks should be okay. Move them somewhere else and try running the game. If it works, you can delete the .paks and save yourself some space. If it doesn't work, you may have to use the files-first override (described in the unpacker readme, I think) just in case the program is still set on reading from the .paks, or move them back if that doesn't work either.