Intercalation is a promising technique to modify the structural and electronic properties of 2D materials on the wafer scale for future electronic device applications. Yet, few reports to date demonstrate 2D intercalation as a viable technique on this scale. Spurred by recent demonstrations of mm-scale sensors, we use hydrogen intercalated quasi-freestanding bilayer graphene (hQBG) grown on 6H-SiC(0001), to understand the electronic properties of a large-area (16 mm2) device. To do this, we first analyze Shubnikov-de Haas (SdH) oscillations and weak localization, permitting determination of the Fermi level, cyclotron effective mass, and quantum scattering time. Our transport results indicate that at low temperature, scattering in hQBG is dominated by charged impurities and electron-electron interactions. Using low- temperature scanning tunneling microscopy and spectroscopy (STS), we investigate the source of the charged impurities on the nm-scale via observation of Friedel oscillations. Comparison to theory suggests that the Friedel oscillations we observe are caused by hydrogen vacancies underneath the hQBG. Furthermore, STS measurements demonstrate that hydrogen vacancies in the hQBG have an extremely localized effect on the local density of states, such that the Fermi level of the hQBG is only affected directly above the location of the defect. Hence, we find that the calculated Fermi level from SdH oscillations on the millimeter scale agrees with the value measured locally on the nanometer scale with STS measurements.