In this work, we perform the first systematic investigation of effects of the presence of dark matter on r-mode oscillations in neutron stars (NSs). Using a self-interacting dark matter (DM) model based on the neutron decay anomaly and a hadronic model obtained from the posterior distribution of a recent Bayesian analysis, we impose constraints on the DM self-interaction strength using recent multimessenger astrophysical observations. We also put new constraints on the DM fraction for this model of DM. The constrained DM interaction strength is then used to estimate DM self-interaction cross section and shear viscosity resulting from DM, which is found to be several orders of magnitude smaller than shear viscosity due to hadronic matter. Assuming chemical equilibrium among DM fermions and neutrons, we estimate the bulk viscosity resulting from the dark decay of neutrons considering different scenarios for the temperature dependence of the reaction rate and investigate the effect on the r-mode instability window. We conclude that DM shear and bulk viscosity may significantly modify the r-mode instability window compared with the minimal hadronic viscosities, depending on the temperature dependence of the process. We also found that for the window to be compatible with the X-ray and pulsar observational data, the rate for the dark decay process must be fast.