I have hit around 10 Morse code bunkers and I have only found 3 that actually had the loot box. I would assume if the bunker was already picked it would have the empty storage box sitting there still but almost all the bunkers I have seen are completely missing the loot crate.

Check any Morse code bunker and it’s likely empty besides a few random military items on the ground

Expected result is to find a loot crate in every Morse code bunker.