We study lensing magnification of source galaxies by intervening galaxy groups and clusters using a halo model. Halos are modeled with truncated NFW profiles with ellipticity added to their lensing potential and propagated to observable lensing statistics. We present the formalism to calculate observable effects due to a distribution of halos of different masses at different redshifts along the l ine of sight. We calculate the effects of magnification on the number counts of high-redshift galaxies. Using BLAST survey data for submillimeter galaxies (SMGs), we find that magnification affects the steep, high flux par t of the counts by about 60%. The effect becomes much stronger if the intrinsic distribution is signi ficantly steeper than observed. We also consider the effect of this high-redshift galaxy population on contaminating the Sunyaev-Zel'dovich (SZ) signal of massive clusters using the halo model approach. We find that for the majority of clusters expected to be detected with ongoing SZ surveys, there is significant contamination from the Poisson noise due to background SMGs. This contr ibution can be comparable to the SZ increment for typical clusters and can also contaminate the SZ decrement of low mass clusters. Thus SZ observations, especially for the increment part of the SZ spectrum, need to include careful modeling of this irreducible contamination for mass estimation. Lensing further enhances the contamination, especially close to the cores of massive clusters and for very disturbed clusters with large magnification cross-section.