So with the fact that warheads ignore the shields of the ship they are attached to you can, with a simple clock, make a ship that will explode as soon as it spawns. Set this ship to be enemy usable and it will spawn with waves of pirates as if those pirates just took out an innocent transport.
Now the spawning mechanics of the game are a not entirely clear to me and this is just a proof of concept. It will take more tests to see if this is a viable solution to add these types on "instances" into the game. Set the wrong ship as a derelict and it will spawn too often or not at all.
Of course server ops can spawn these ships in the middle of nowhere as treasure hunts. They can be loaded with "rare" blocks in cargo holds... well as rare as any block in this game is anyway.