There is observational evidence that nuclear winds and X-rays can heavily influence the physical conditions and chemical abundances of molecular gas in the circumnuclear disks (CND) of Active Galactic Nuclei (AGN). In this paper we probe the chemical status of molecular gas in the CND of NGC 1068, a prototypical Seyfert 2 galaxy. Precedent claims that the chemistry of molecular gas in the nucleus of NGC 1068 is abnormal by galactic standards were based on the high HCN/CO luminosity ratio measured in the CND. Results from new observations obtained in this survey have served to derive abundances of molecular species such as SiO, CN, HCO⁺, HOC⁺, H¹³CO⁺ and HCO. These estimates are complemented by a re-evaluation of molecular abundances for HCN, CS and CO, based on previously published single-dish and interferometer observations of NGC 1068. We report on the first detection of SiO emission in the CND of NGC 1068. The estimated large abundance of SiO in the CND, X(SiO)˜(5-10)×10^-9, cannot be attributed to shocks related to star formation, as there is little evidence of a recent starburst in the nucleus of NGC 1068. Alternatively, we propose that silicon chemistry is driven by intense X-ray processing of molecular gas. We also report on the first extragalactic detection of the reactive ion HOC⁺. Most remarkably, the estimated HCO⁺/HOC⁺ abundance ratio in the nucleus of NGC 1068, ˜30-80, is the smallest ever measured in molecular gas. The abundances derived for all molecules that have been the subject of this survey are compared with the predictions of models invoking either oxygen-depletion or X-ray chemistry in molecular gas. Our conclusions favour an overall scenario where the CND of NGC 1068 has become a giant X-ray Dominated Region (XDR).