Unmanned Aerial Vehicle (UAV) thermal imagery is rapidly becoming an essential tool in precision agriculture. Its ability to enable widespread crop status assessment is increasingly critical, given escalating water demands and limited resources, which drive the need for optimizing water use and crop yield through well-planned irrigation and vegetation management. Despite advancements in crop assessment methodologies, including the use of vegetation indices, 2D mapping, and 3D point cloud technologies, some aspects remain less understood. For instance, mission plans often capture nadir and oblique images simultaneously, which can be time- and resource-intensive, without a clear understanding of each image type’s impact. This issue is particularly critical for crops with specific growth patterns, such as woody crops, which grow vertically. This research aims to investigate the role of nadir and oblique images in the generation of CWSI (Crop Water Stress Index) maps and CWSI point clouds, that is 2D and 3D products, in woody crops for precision agriculture. To this end, products were generated using Agisoft Metashape, ArcGIS Pro, and CloudCompare to explore the effects of various flight configurations on the final outcome, seeking to identify the most efficient workflow for each remote sensing product. A linear regression analysis reveals that, for generating 2D products (orthomosaics), combining flight angles is redundant, while 3D products (point clouds) are generated equally from nadir and oblique images. Volume calculations show that combining nadir and oblique flights yields the most accurate results for CWSI point clouds compared to LiDAR in terms of geometric representation (R2 = 0.72), followed by the nadir flight (R2 = 0.68), and, finally, the oblique flight (R2 = 0.54). Thus, point clouds offer a fuller perspective of the canopy. To our knowledge, this is the first time that CWSI point clouds have been used for precision viticulture, and this knowledge can aid farm managers, technicians, or UAV pilots in optimizing the capture of UAV image datasets in line with their specific goals.