Because FR'd foals are deleted from the game, they are also deleted from the report. It's my understanding that a stud with all foals FR'd will show as having no progeny.
What Rocky said. This is why stud owners will ask that you FR foals below a certain rating; so they will be removed from the progeny of that horse and thus not count towards the overall quality of that horse throws, which is important for trying to get a horse on the leaderboards.