We present a quantum transport study of two- and three-terminal carbon nanotube (CNT) based junctions. We concentrate our analysis on functionalized and recapped zig-zag CNTs exhibiting peculiar surface electronic states localized at the zig-zag cut and at the cap defect atoms respectively. We calculate the linear conductance by means of the Green function technique, within a pi-orbital description of the carbon network, and show the interplay between these peculiar localized states and the open transport channels through the device. In correspondence of the energies of the localized states, the conductance behavior shows a Fano-like resonance. Possible experimental conditions and setup in which such effect could be detected are also discussed.