What a great project!
As for why it died, rather than it being shot down, what about failure of the balloon due to UV/sunlight degradation of the balloon skin? Or water penetration of the electronics. Something really simple like 'string broke.' Or icing up and sinking to the ground due to over-weight.
Or, if the military did notice it and act, could well have been done using the new anti-missile laser systems.
Suggestions for next time:
- A power down/wakeup timer and enough battery capacity for at least a few fixes during the night.
- A message on the outside "If found, please contact ..." (in a few different languages)
And in the the probably too hard or too heavy category:
- Tiny camera from a mobile phone, and ability to transmit images.
- A small reserve battery, some means of detecting falling, low altitude or on ground, to allow a final burst giving last known position. Then a small RF pinger - very short burst every hour, for several days. Give the last known location and ping frequency to the geocaching community and see if they can find it.