I don't know about really cross field applications so far, but the Deficiency Zero Theorem has been applied recently by Rendall to a model of the NFAT signalling pathway by Salazar and Höfer in T-cells and by Sontag for McKeithan’s kinetic proofreading model of T cell activation. So you have some applications in biochemistry or immunology.
Also Horn and Jackson quite early have given examples for certain categories of networks with deficiency zero in "Horn, F. (1973a). Necessary and sufficient conditions for complex balancing in chemical kinetics. Arch. Rat/. Mech. Anal., 49, 172-86." and "Horn, F. & Jackson, R. (1972). General mass action kinetics. Arch. Rat/. Mech. Anal., 47,81-116.".