Thermally sprayed metallic coatings on carbon fiber-reinforced polymer (CFRP) substrates often contain pores and microstructural defects that can reduce adhesion, durability, and protective performance. In this study, a hybrid graphene nanoplatelet (GNP)-fullerene C60 reinforced epoxy coating was applied to HVOF-metallized CFRP, while a carbon nanotube (CNT)-based surface treatment was used to modify surface wettability. Micro-CT and SEM analyses indicated morphological changes consistent with partial coverage of accessible surface-connected defects and modification of the metallized layer surface. Pull-off adhesion strength increased from 320 psi to 650 psi, accompanied by a shift from adhesive to cohesive failure. The optimal nanofiller formulation improved tensile strength from approximately 25 MPa to 56 MPa (124%) and Young’s modulus by approximately 47% compared with neat epoxy. Abrasion testing showed more than 50% reduction in mass loss, and electrochemical impedance spectroscopy indicated improved barrier performance after 200 h of salt spray exposure. CNT surface modification transformed the coating from hydrophilic to superhydrophobic behavior, achieving water contact angles above 155°, delaying ice formation, and reducing ice accumulation. These results indicate that combining hybrid nanocomposite coatings with CNT functionalization can improve mechanical, protective, and surface-functional performance of HVOF-metallized CFRP systems under the laboratory conditions investigated.