Greg pointed out that we are using Ø (Latin Capital Letter O with Stroke, U+00D8) for our zero morpheme marker, rather than ∅ (Empty Set, U+2205). The latter is noted in the Unicode character map as the one used in linguistics to indicate a null morpheme or phonological zero.
We have at least been consistent in our use of the former! We may not have known the Empty Set character existed when we chose the other one in 2010, or it may have been a font-based choice. (I'm using Aboriginal Sans in Oxygen right now, and the Empty Set character doesn't display properly.)
Martin will add this change to his list of global changes to make when improving our current encoding, if we can be assured of fonts that include Empty Set along with all the other special characters we need.