We present resistivity and magnetization measurements on proton-irradiated crystals demonstrating that the superconducting state in the doped topological superconductor Nb$_x$Bi$_2$Se$_3$ (x = 0.25) is surprisingly robust against disorder-induced electron scattering. The superconducting transition temperature $T_c$ decreases without indication of saturation with increasing defect concentration, and the corresponding scattering rates far surpass expectations based on conventional theory. The low-temperature variation of the London penetration depth $Deltalambda(T)$ follows a power law ($Deltalambda(T)sim T^2$) indicating the presence of symmetry-protected point nodes. Our results are consistent with the proposed robust nematic $E_u$ pairing state in this material.