Background/Objectives: Sinonasal anatomical variations, particularly Haller cells (HCs) and the accessory maxillary ostium (AMO), are critical structural factors that may increase surgical risks in dental and otorhinolaryngological (ENT) procedures and predispose individuals to chronic sinusitis. This study aimed to investigate the relationship between HCs, AMO dimensions, maxillary sinus ostium, and sinus pathologies using cone-beam computed tomography (CBCT). Methods: In this cross-sectional retrospective study, CBCT images of 443 patients (226 males, mean age 48.4 +/- 15.4 years; 217 females, mean age 46.1 +/- 15.2 years) were analyzed. The presence of HCs, AMO, ostium narrowing, and ostium obstruction were recorded, along with ostium dimensions. Relationships between these variations and sinus pathologies were statistically evaluated, with a p-value < 0.05 considered significant. Results: HC prevalence was 34.5% on the right and 39.5% on the left, while AMO was present in 39.5% on the right and 34.5% on the left. Bilateral AMO was significantly associated with localized mucosal thickening, and partial opacification was more common in cases with ostium obstruction. Significant relationships were observed between HC presence and ostium narrowing. While HCs and ostium narrowing did not significantly influence maxillary sinus pathologies, sex (right OR = 0.335; left OR = 0.384; p < 0.001) and the AMO (right OR = 1.698, p = 0.018; left OR = 1.713, p = 0.014) were found to have a significant impact. Conclusions: It was concluded that (i) HCs may contribute to ostium narrowing and impaired sinus drainage, thereby increasing the risk of chronic sinusitis; (ii) the presence of a bilateral AMO is strongly associated with localized mucosal thickening; (iii) sex and the presence of an AMO emerge as independent predictors of maxillary sinus pathologies; and (iv) the careful evaluation of these anatomical variations using CBCT can support multidisciplinary treatment planning in both dental and ENT practice, enhance surgical safety, and help minimize postoperative complications.