To be fair, "Element Zero" was so named because it behaves like a pseudo-atom, with a quark structure in the center around which one or more electrons would orbit; it can be charged and it can be ionized, it can enter one of the normal phases of matter (solid, liquid, gas, though it's happiest as a gas or plasma) and it can form compounds with other elements both in its natural and refined state.
Though it would have some very odd properties, I don't think its existence would change much about the laws of physics or the nature of reality as we know it. All the theoretical forms of quark matter can only form in or around neutron stars or black holes; in Mass Effect, Element Zero is deposited on the surfaces of planets and asteroids in the vicinity of supernova explosions. It would be, by its very nature, very difficult to find unless you were looking for it in exactly the right spot.
OTOH, I've heard it theorized by some physicists that Dark Matter could easily be a form of electrically neutral quark matter in a long-term stable form that never got the chance to form real atoms and now never will. My customary response to all of these theories is "dark matter is bullshit" but this one deserves honorable mention for originality, IMO.