Using Langevin molecular dynamics simulations we study relaxation processes of interacting skyrmion systems with and without quenched disorder. Using the typical diffusion length as the time-dependent length characterizing the relaxation process, we find that clean systems always display dynamical scaling, and this even in cases where the typical length is not a simple power law of time. In the presence of the Magnus force, two different regimes are identified as a function of the noise strength. The Magnus force has also a major impact when attractive pinning sites are present, as this velocity-dependent force helps skyrmions to bend around defects and avoid caging effects. With the exception of the limit of large noise, for which dynamical scaling persists even in the presence of quenched disorder, attractive pinning sites capture a substantial fraction of skyrmions which results in a complex behavior of the two-time autocorrelation function that is not reproduced by a simple aging scaling ansatz.