Gallium nitride (GaN) homoepitaxial layers grown on Ammonothermal (Am-GaN) and Hydride Vapor Phase Epitaxy (HVPE-GaN) substrates were comparatively investigated to assess the impact of substrate quality on structural and electrical properties. Despite both substrates exhibiting smooth surfaces, the GaN layers grown on HVPE-GaN substrates exhibit higher surface roughness, defect density, and tensile strain than their Am-GaN counterparts. Vertical Ni/GaN Schottky diodes were fabricated, showing thermionic emission (TE) as the dominant mechanism in the forward current-voltage (I-V) characteristics, with homogeneous barrier heights of 1.11 eV and 0.90 eV for Am-GaN and HVPE-GaN, respectively. Under reverse bias, the Am-GaN devices I-V characteristics are well described by thermionic field emission (TFE), whereas HVPE-GaN diodes exhibit a mixed conduction mechanism involving both TFE and trap-assisted tunneling (TAT), leading to higher leakage currents. These results demonstrate a strong correlation between substrate growth technique, epitaxial quality, and Schottky barrier properties, highlighting the role of substrate in device performance.