They're supposed to be quartz crystal. I'd like to see them replace Applied Energistics' Quartz through the Forge Ore Dictionary, to make them more useful and reduce duplication (why have two separate, but incompatible, versions of quartz in the game?).
I also agree they shouldn't destroy items (I never knew about that until reading this post). Perhaps a solution is to have the crystals form inside of a standard ore block like in Applied Energistics, but have the block drop the Xycraft crystal as an item, which can then be placed in the world if desired. This would easily solve the rendering issue (the ore would just need a texture), and prevent most inadvertent item destruction, but keep the interesting model and mob trap functionality.
AE quartz has in the latest update had its name changed to something else still something quartz but not just quartz anymore and its not compatible with nether quartz. Also I would say quartz crystals are a lot more abundant than AE quartz (not to mention that you get quartz dust too from AE quartz) meaning that if they were interchangeable it would throw off the balance of AE.