Inorganic-organic hybrid materials that combine both Polyoxometalates (POMs) and metal ion coordinating subunits (CSUs) represent promising multifunctional materials. Though their individual components are often biologically active, utilization of hybrid materials in bioassays significantly depends on the functionalization method and thus resulting stability of the system. Quite intriguingly, these aspects were very scarcely studied in hybrid materials based on the Wells-Dawson POM (WD POM) scaffold and remain unknown. We chose two model WD POM hybrid systems to establish how the functionalization mode (ionic vs. covalent) affects their stability in biological medium and interaction with nucleic acids. The synthetic scope and limitations of the covalent POM-terpyridine hybrids were demonstrated and compared with the ionic Complex-Decorated Surfactant Encapsulated-Clusters (CD-SECs) hybrids. The nature of POM and CSU binding can be utilized to modulate the stability of the hybrid and the extent of DNA binding. The above systems show potential to behave as model cargo-platforms for potential utilization in medicine and pharmacy.