Would it be possible to cut a hole out of the "seat" portion and use it for storage inside the bench area? You'd have to have a larger piece of wood to put back over the hole to hide your goodies along with a window seat cushion. No one would know you had anything stored under the cushion.
Or could you cut out the front panel (where you heels hit the wood when you sit on the window seat) and frame it out for storage there?