The issue was raised in June here (https://forums.sinsofasolarempire2.com/536578/ship-graveyard-planet-items-error#replies) and Zabik_2 said he'd check with the team about their vision for the issue but the situation seems to be unchanged. 

It remains something of a garbage colonisable, but the TEC can place the Experimental Economics Lab, Secret Weapons Lab, or Pirate Mercenary Base, Advent can place the Shrine of Harmony, Shrine of Hostility, Silent Monastery, or Telepathic Relay, and the Vasari remain unable to place anything in the slots.

I haven't checked all the Minor Faction options e.g. Smugglers Den, Aluxian Economic Advisor, Aluxian Governor-Scion, Frontier Colony Uplink, Frontier Adaption Lab, or Phase Crystalizer, but I'm skeptical. The Unassailable Fortress definitely wasn't an option. 

I also haven't checked the Relativistic Factories, Data Archive, Tachyon Comms Relay, Manifest Dominion, or Matter Synthesizer, but the odds of getting any of these are fairly low, and in the case of Relativistic Factories, rather a waste since it only affects the gravity well it's placed in, and Ship Graveyard can only hold 2 shipyards at a maximum (5 civilian slots) - and this would be akin to any planet with 4 shipyards.

Obviously it's not a critical issue - Ship Graveyards are rare, but it's slightly annoying to get a colonisable system that basically isn't worth colonising!