This study deals with the investigation of the tensile and shear behavior of connected carbon nanotubes (CNTs) with parallel longitudinal axes by performing several computational tests. In particular, the effect of imperfections on the mechanical properties, i.e. Young's modulus and shear modulus, of these nanoconfigurations was analyzed. For this purpose, straight hetero-junctions were simulated in their perfect form and different boundary conditions were considered. In the second phase the three most likely atomic defects, i.e. impurities (doping with Si atoms), vacant sites (carbon vacancy) and introduced perturbations of the ideal geometry in different amounts to the perfect models, were simulated. Finally, the mechanical properties of imperfect hetero-junctions were numerically evaluated and compared with the behavior of perfect ones. It was concluded that the existence of any type of imperfections in the structure of connected CNTs leads to a reduction in the Young's modulus as well as the shear modulus, and as a result, lower stiffness of these straight nanostructures.