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The chemistry of proto-planetary disks is thought to be dominated by two major processes: photodissociation near the disk surface, and depletion on dust grains in the disk mid-plane, resulting in a layered structure with molecules located in a warm layer above the disk mid-plane. We attempt here to confront this warm molecular layer model prediction with the distribution of two key molecules for dissociation processes: CN and HCN. Using the IRAM Plateau de Bure interferometer, we obtained high spatial and spectral resolution images of the CN J=2-1 and HCN J=1-0 lines in the disks surrounding the two T-Tauri DM Tau and LkCa 15 and the Herbig Ae MWC 480. Disk properties are derived assuming power law distributions. The hyperfine structure of the observed transitions allows us to constrain the line opacities and excitation temperatures. We compare the observational results with predictions from existing chemical models, and use a simple PDR model (without freeze-out of molecules on grains and surface chemistry) to illustrate dependencies on UV field strength, grain size and gas-to-dust ratio. We also evaluate the impact of Lyman alpha radiation. The temperature ordering follows the trend found from CO lines, with DM Tau being the coldest object and MWC 480 the warmest. Although CN indicates somewhat higher excitation temperatures than HCN, the derived values in the T-Tauri disks are very low (8-10 K). They agree with results obtained from CCH, and are in contradiction with thermal and chemical model predictions. These very low temperatures, as well as geometrical constraints, suggest that substantial amounts of CN and HCN remain in the gas phase close to the disk mid-plane, and that this mid-plane is quite cold. The observed CN/HCN ratio (5-10) is in better agreement with the existence of large grains, and possibly also a substantial contribution of Lyman alpha radiation.