Fused Deposition Modeling (FDM) inherently induces inter-raster voids, which act as stress concentrators and significantly compromise the mechanical and dynamic integrity of printed components. This research presents a novel hybrid framework that integrates semi-empirical characterization with analytical modeling to quantify porosity and predict its effect on the vibrational behavior of Polylactic Acid (PLA) beams. Moving beyond simplified circular approximations, a data-driven geometric model employing the Superellipse function was developed to map the actual void morphology based on Scanning Electron Microscopy (SEM) and G-code toolpaths. These quantitative porosity estimates were subsequently incorporated into a stiffness-reduction constitutive model within the context of Classical Laminate Theory (CLT). Experimental validation, utilizing Digital Image Correlation (DIC) and modal analysis, confirmed the model's accuracy (porosity range: 1.3%–1.9%). Crucially, the findings reveal a direction-dependent frequency response: while the 0° raster angle maintains relative frequency stability due to a balanced reduction in mass and stiffness, the 90° raster angle exhibits a disproportionate stiffness decay, resulting in a precipitous drop in natural frequencies (up to 27%). This study establishes porosity not merely as a defect, but as a critical design parameter for predicting the dynamic performance of FDM structures.