The objective of this study was to compare the distribution of stress in the maxillary bone, dental implants, and prosthetic components supporting implant-supported maxillary overdentures with partial palatal coverage, in both splinted and unsplinted designs. Two models of maxillary overdentures were designed using the Exocad Dental CAD program, which included cancellous and cortical bone. The complete denture design and abutments (locator abutments in the unsplinted and Hader bar with Vertix attachments placed distally in the splinted variant) were also designed. The denture material was PEEK (Polyetheretherketone), and the method used to analyze patient-specific 3D X-ray scans was 3D QCT/FEA (three-dimensional quantitative computed tomography-based finite element analysis). Loading was divided into three load cases, in the frontal region (both incisors of the denture) and distal region (both molars and first premolar of the denture). The forces applied were 150 N with an oblique component with a buccal inclination of 35° in the frontal region, and 600 N with a buccal inclination of 5° (molars) or solely vertical (premolar) in the distal region. The model with locator abutments showed higher stresses in all load cases in both analyzed implant variants and in the maxilla. The differences in stress distribution between the splinted and unsplinted variants were more significant in the distal region. According to the results of the present study, the amount of stress in bone tissue and dental implant parts was smaller in the splinted, bar-retained variant. The findings of this study can be useful in selecting the appropriate prosthetic design for implant-supported maxillary overdentures with partial palatal coverage.