Context. The mid-infrared (MIR) emission of molecules such as H2O, HCN, OH, CO2, and C2H2, has been identified in the Spitzer Infrared Spectrograph (IRS) spectra of many protoplanetary disks. According to the modelling results, the blend strengths are affected by different disk properties such as the gas mass and dust content in the disks. An observational correlation between HCN and water blend fluxes has been noted, specifically related to a changing disk gas mass. Aims. We aim to find out whether the explanation for the observed flux correlation between HCN and water in the MIR could also be attributed to other properties and processes taking place in disks, such as the evolution of dust grains. We also consider what the consequences of these results would be in relation to the disk evolution. Methods. We used pre-existing ProDiMo radiation thermal-chemical disk models exploring a range of properties such as the disk gas mass, disk inner radius, dust size power law distribution, and, finally, time-dependent dust evolution. From these models, we computed the MIR fluxes of HCN and H2O blends. Simultaneously, we derived the spectral indices from the simulated spectral energy distributions (SEDs) in the Spitzer IRS regime. Finally, we compared these quantities with the observed data. Results. The MIR blend fluxes correlation between HCN and water can be explained as a consequence of dust evolution, namely, changes in the dust MIR opacity. Other disk properties, such as the disk inner radius and the disk flaring angle, can only partially cover the dynamic range of the HCN and water blend observations. At the same time, the dynamic range of the MIR SED slopes is better reproduced by the disk structure (e.g. inner radius, flaring) than by the dust evolution. Our model series do not reproduce the observed trend between continuum flux at 850 µm and the MIR HCN/H2O blend ratio. However, our models show that this continuum flux is not a unique indicator of disk mass and it should therefore be used jointly with complementary observational data for optimal results. Conclusions. The presence of an anti-correlation between MIR H2O blend fluxes and the MIR SED is consistent with a scenario where dust evolves in disks, producing lower opacity and stronger features in the Spitzer spectral regime, while the gas eventually becomes depleted at a later stage, leaving behind an inner cavity in the disk.