We have combined large-scale, $\Gamma$-point electronic-structure calculations with the maximally localized Wannier functions approach to calculate efficiently the band structure and the quantum conductance of complex systems containing thousands of atoms while maintaining full first-principles accuracy. We have applied this approach to study covalent functionalizations in metallic single-walled carbon nanotubes. We find that the band structure around the Fermi energy is much less dependent on the chemical nature of the ligands than on the $s{p}^3$ functionalization pattern disrupting the conjugation network. Common aryl functionalizations are more stable when paired with saturating hydrogens; even when paired, they still act as strong scattering centers that degrade the ballistic conductance of the nanotubes already at low degrees of coverage.