This is something I've seen off and on ever since pirates were introduced to the game. Ocassionly, and randomly, a Ship Graveyard will NOT be defended by pirates. I was never sure if this was Working as Intended or not, so I never sent in a ticket on the issue. Also, because it was so random that it didn't always survive a restart/reload it made it difficult to show the bug in action.
But after looking at the code and after playing with a mod that also had its own custom Ship Graveyard encounters, I'm fairly sure this is indeed a bug.
So I have just sent in a ticket on this (#JIB-999-22474) where I have SIX ships capable of surveying anomalies parked next to six Ship Graveyards. So far, for me at least, one of them always does not trigger a Ship Graveyard encounter no matter how many times I reload or restart (though they aren't always the same Ship Graveyard).
Hopefully this will help track down this random bug. 
Turns out this isn't a bug at all, as I missed the "Encounter Chance" tag.
Whoops. Egg's on my face now. Please disregard this and the ticket I sent, SD (already posted on the ticket "thread" to disregard it).