A seismic modeling system may include a seismic model data storage device, and a processor cooperating with the seismic model data storage device to transform a seismic model spatial domain data set associated with a given region into a seismic frequency domain data set, where the given region includes a suspect region, transform a seismic model spatial domain data subset associated with the suspect region into a seismic frequency domain data subset, and perform inpainting of the seismic frequency domain data subset based upon the seismic frequency domain data set. The processor may further convert the inpainted seismic frequency domain data subset into an inpainted spatial domain data subset, and substitute the inpainted spatial domain data subset for the seismic model spatial domain data subset associated with the suspect region in the seismic model spatial domain data set associated with the given region.